I was thinking about this very question as I was looking through your mod, Foraven. My major concern is that it creates an optimum fleet composition.
An air-defence warship is still expected to be able to engage other surface combatants, and submarines, and land marines, and so on. It just does it slightly worse than the dedicated hull. In the grand scheme of things, the difference between the various types of destroyer in use by the Royal Navy is probably more down to module choice than fundamental hull design. A British Type-23 anti-submarine frigate is about 4,900 tonnes, whilst a Type-42 guided-missile destroyer was 4,500 tonnes. These are, in Stellaris terms, both "Destroyer"-class hulls. The USN Ticonderoga-class guided-missile cruiser is almost double the size at 9,600 tonnes (According to the USN, and Stellaris, I'd call this a Cruiser). It does the same thing as the Type-42, but is of a different hull class.
This example is instructive to me. It suggests to me that hull-type and role are independent of each other. Just as you can have super-carriers, carriers, and aircraft-cruisers, you can have any hull-class doing any role.
The way I am approaching this issue in my ship-components mod is as follows (I'm still stuck on working my way through Master of Orion-inspired components and crew types):
1) Make variable-size PD mounts (meaning that you can have something that fits into M and L slots too)
2) Make more modules that provide more slots
3) Make components that provide a bonus to PD-fire-rate / accuracy.
4) Make more intermediate PD-type weapons rather than the 3 vanilla weapon-types
Thus you provide the option for players to make anything from PD-zilla to a jack-of-all-trades, as their whim and budget allows.
EDIT: What convinces me that a role should be independent of a hull-size is the idea of the PD-destroyer. If I want to make a PD-battleship, you're telling me that the ship is WORSE even though it has more guns?