Are Cruisers and Battleships supposed to view penetrators as a real threat?
Corvettes start off with 300 base Hull points and gain +100 Hull each at Tier-1 Improved and Tier-2 Advanced Hull Reinforcement. They have 3 S-slot utilities, which scale by Shield or Armor Tier to be 50 points each at Tier-0, then to ~30% more per Tier or 65 @ T1, 85 @ T2, etc. At T0, a base Corvette and its 3 S-slots of T0 Shields and/or Armor would be 300 Hull and 150 S/A, or Hull equal to 2.00 S/A or 0.67 of the total defenses. At T1, it's now 400 Hull (IHR) and 3 x 65 = 185 S/A, or 2.16 HSA and 0.68 HTD; T2 is 500 Hull (AHR) and 3 x 85 = 255 S/A, or 1.96 HSA and 0.66 HTD. At T5 without repeatables, it's still 500 Hull and now 3 x 185 = 555 S/A, or only 0.90 HSA and 0.47 HTD; with 10 repeatables for Shields and Armor, it's again 500 Hull and 832.5 S/A, or all the way down to 0.60 HSA and 0.38 HTD. (Tier-5 Shields (Dark Matter Deflectors) are a salvage tech from Fallen Empires, while T5 Armor (Dragonscale Armor) is a salvage tech from either the Ether Drake or Sky Dragon, so may not always be available.)
Considering penetrator weapons of any kind don't show up until Tier-2, it doesn't really matter what the ratios are below there. At T2, a penetrator would have to do at least 66% of the base damage of the non-penetrating weapons to be competitive against Corvettes, assuming the non-pen weapons don't gain a vs.Hull advantage (and it doesn't account for the platoon advantage by pairing Mass Drivers and Lasers to get through S/A). A T2 S-slot Disruptor averages 1.55 base damage per day compared to a T2 S-slot UV Laser at 3.61 DPD - this is only 43% of the Laser's damage. Does it get better as tech Tier increases? A T4 Corvette is 500 Hull and 435 S/A, or 1.15 HSA and 0.53 HTD - the ratio for the weapons has to be at least 53% to be competitive here. A T5 non-repeated Corvette is close at 47%, and finally at T5 + 10x repeatables the penetrators are finally successful by clearing the 38% damage ratio. Despite the pathetic 30 Range (-10 vs. Laser, -20 vs. Mass Driver) and the remarkable 60 Tracking (+10 vs. either), penetrators clearly aren't intended for damaging Corvettes.
Destroyers enter the game as a Tier-2 technology, and start off with 800* base Hull and gain +200 Hull each at T2 IHR and T3 AHR. They have 6 S-slot utilities, which have the same scaling as with Corvettes above. At the end of Tier-2, a Destroyer with IHR and its 6 S-slots of T2 Shields and/or Armor would be 1000 Hull and 510 S/A, or 1.96 HSA and 0.66 HTD. At T3, it's 1200 Hull and 660 S/A, or 1.82 HSA and 0.65 HTD; at T4, it's still 1200 Hull and 870 S/A, or 1.38 HSA and 0.58 HTD. At T5 before repeatables, it's again 1200 Hull, 1110 S/A, 1.08 HSA, and 0.52 HTD; with 10x repeatables, it's 1200 Hull, 1665 S/A, 0.72 HSA, and 0.42 HTD. The weapons aren't any different than above, whether S-slot or M-slot, with regard to the ratios between those of the same size, so again the only time penetrators are competitive is after all repeatables - penetrators clearly aren't intended for damaging Destroyers.
* Why do Destroyers get such an outsized increase over the Corvette in base Hull? A pure doubling of Hull would be just 600 but would align with the IHR/AHR improvements doubling. If the square root of 6 (~2.45) increase common to all of the weapon and utility slot size increases was in play, then 735 Hull points would be appropriate (maybe bump to 750 for a more round number). More on this issue later...
Cruisers enter the game as a Tier-3 technology, and start off with just 1800 base Hull and gain +400 Hull each at T3 IHR and T4 AHR. Instead of the +167% Hull increase over the Destroyer that the DD got over the Corvette, or even the expected +145% increase relative to weapons and utilities, the Cruiser only gets 125% (though it is strangely exactly 6x the Corvette Hull). Because of the 1/3, 1/2, 1/6 section split for Cruisers (versus 2/3 1/3 for Destroyers and 1/1 for Corvettes), Cruisers don't get access to X-slot weapons (natural size progression over Destroyers with L-slots), and instead just get a quantity doubling - to try to make up for this, Cruisers were given 8 M-slot utilities instead of 6, which will skew HSA and HTD further downward (with the skew toward utilities, why wasn't the Hull increase even bigger?). At the end of Tier-3, they have 2200 Hull and 2200 S/A, or 1.00 HSA and 0.50 HTD (compared to 0.65 for DDs); at T4, it's 2600 Hull and 2920 S/A, or 0.89 HSA and 0.47 HTD. At T5 before repeatables, it's again 2600 Hull, 3720 S/A, 0.70 HSA, and 0.41 HTD; with repeatables it's 2600 Hull, 5580 S/A, 0.47 HSA, and 0.32 HTD.
But now we're dealing with a gap in the weapons - the Disruptor line of penetrators only goes up to M-slot, while the Lasers line includes L-slots. The only L-slot penetrator is Cloud Lightning, which is both a salvage tech and unimprovable beyond Tier-2. The exercise for comparing M-slots is pretty similar to above with Destroyers, and would seem to indicate a legitimate concern for Cruisers, with T4 @ 47% being an outside shot, T5 before @ 41% being even money, and T5 after @ 32% being a slam dunk. Cloud Lightning at 11.41 DPD compares to a T2 L-slot UV Laser at 21.71 DPD or 53%, which would be hopeful if Cruisers were available at T2, but instead it compares to T3 L-slot X-Ray Laser at 28.17 DPD or 41%. T4 is the Gamma Laser at 36.97 DPD or 31%, which means that, despite a more favorable initial damage rate and the plummet in defensive ratios for the Cruiser, Cloud Lightning is no more competitive against Cruisers than any of the Disruptors are versus Corvettes or Destroyers.
Last among the standard hull sizes, Battleships enter the game as a Tier-4 technology, and start off with just 3000 base Hull and gain +800 Hull each at T4 IHR and T5 AHR. If the Destroyer base Hull is supposed to be correct, and a Battleship has 6x the S/A points, the Battleship maybe should be 4800 base Hull to keep pace, but instead is at only 3.75x. Even with only the more-typical 6 L-slot utilities (versus the 8 M-slots for Cruisers), Battleships have even more skewed ratios, with the end of T4 having them at 3800 Hull and 5220 S/A, or 0.73 HSA and 0.42 HTD. At T5 before repeatables, it's 4600 Hull, 6660 S/A, 0.69 HSA, and 0.41 HTD; with repeatables, it's again 4600 Hull, 9990 S/A, 0.46 HSA, and 0.32 HTD. Very similar to Cruisers, Battleships would seem to be vulnerable to penetrators, if only they could keep pace, but they don't.
Now a Cruiser or Battleship might take advantage of Crystal-Infused (275/660 Hull) or Crystal-Forged Plating (465/1110). Swapping out just one S/A for a Tier-appropriate Plating would boost survivability versus penetrators. A T3 Cruiser with one Plating and 7 S/A would have 2475 Hull, 1925 S/A, 1.29 HSA, and 0.56 HTD (vs. 1.00 and 0.50 above); T5 with repeatables would be 3065 Hull, 4867.5 S/A, 0.63 HSA, and 0.39 HTD (vs. 0.47 and 0.32). A T4 Battleship with one Plating and 5 S/A would have 4910 Hull, 4350 S/A, 1.13 HSA, and 0.53 HTD (vs. 0.73 and 0.42); T5 with repeatables is 5710 Hull, 8325 S/A, 0.69 HSA, and 0.41 HTD (vs. 0.46 and 0.32). But both sets of Plating require salvage techs, with the first being far more common but the second being more rare than either of the T5 S/A techs. Comparing the Cruiser and Battleship HSA and HTD numbers with 1 Plating to Corvettes and Destroyers without and seeing how close they are to each other, makes me think the Dev-intended defensive configuration is supposed to be exactly that.
Even before we get to X-slots, the existence of the advanced weapons (Proton/Neutron Launchers and Kinetic Batteries/Artillery) makes a mockery of the earlier comparison to Lasers. They're L-slot weapons, with exceptional Range (120-130 vs. 60, although CL maintains 30 Tracking - this is overkill vs. Cruisers and Battleships) and versus-defense ratios. I've previously mapped out
how I thought an L-slot Tier-4+ penetrator would look, but what I came up with is still only 52% of the base damage of a Neutron Launcher, and WAY behind after versus-defense multipliers (especially when platooned with Kinetic Artillery). (My T4+ penetrator, as indicated in its linked post, almost definitely needs to be bumped up in damage to counter the more favorable versus-defense rates of PL/NL and KB/KA over their Laser and Mass Driver peers, but I wasn't sure by how much.)
And now we get to Arc Emitters and Focused Arc Emitters, that have 80.30 and 105.00 base DPD compared to Particle Lances (111.56 DPD, with AE being 72% of that) and Tachyon Lances (148.75, 71%). Do you see something different here? The other X-slot weapons do have even more favorable versus-defense multipliers, but not enough to account entirely for the massive jump in relative-DPD compared to their earlier & smaller peers. Other assessments that have been made with AE/FAE compared to PL/TL or Mega Cannons/Giga Cannons, show AE/FAE behind their peers in a number of defensive configurations when looked at in isolation, but the differences are relatively small. Some assessments include the L-slots filled with Neutron Launchers and Kinetic Artillery, and the AE/FAEs performing poorly because of that, but those do not synergize well with the penetrating AE/FAEs.
So, in answer to the question at the beginning of my comment: yes, but only against X-slot penetrators, only if Plating isn't used, and only once repeatables come into play. As I indicated in the thread linked above, the lack of Tier-4+ L-slot advanced penetrators really gimps any opportunity for penetrators to be competitive with non-penetrators, though even the slightly underpowered proposal I have above does a decent job of bridging the gap. Smaller ships just don't get enough of their total defensive points from Shields & Armor until late along the tech tree for the non-X-slot penetrators to really stand a chance, and even then, they're still capable of forgoing some S/A to bulk up Hull even more.