The Warhammer isn't actually that good though, even with the quirk? It's better than the Catapult-K2 (depending on where you roll with heat management), arguably worse than a Marauder, even if you're not headcapping people, definitely worse than a Black Knight or the Orion in terms of total damage/armor profile. Without the quirk, it would be a relatively worse off mech than the Kurita Catapult.
Making the same mistake as the other guy. It doesn't really matter that the stock isn't that great. It matters what the player can do with it. And the Black Knight is the one that is definitely worse due to it, not the Warhammer.
As for the Annihilator, it would still reach 316 damage (quint AC/5s, quint MLs, max armor, JJs) with HM weapons or the BSC. 316 damage is just about enough to consistently dumpster everything short of an Atlas.
I'd consider that pretty poor damage, actually. Its stock load out replaced with ++damage versions would exceed that. And if you start tossing in Ultras, well, yeah... and then it gets 20% on top of all that. But do notice that the first thing you do is not use a stock Anni, without jump jets and with that crappy armor... and you rip out all of its weaponry and rework the mech from the ground up.
Three of those are noted as being pretty subpar on the tabletop. And "subpar" is being generous to the Vulcan.
And yet those are the ones that get the more balanced, flavorful, quirks.
Now, if something like the 8/12 Cicada got a 20% boost to energy weapon damage, well, no biggie, because that mech is subpar, and there really isn't much you can do with it. Even with coils, it would be somewhat self balancing, since the heat would go up with the damage. With a Warhammer, though, if you want to use some of the bigger energy weapons on a heavy mech, it's the no-brainer. Called shots, aside, of course.
Speaking of the Anni, though, I wonder if we'll get the 1E version... 4 PPCs, 2 extra mediums, 41 heat sinks... Obviously, won't have the quirk, but could function as a super Awesome. Canon timeline-wise, it is pretty close to existing at this point, too, as it comes about post Battle of Misery.