[PvK]

As for massive fighter stacks (unfortunately not moddable away) and large weapon mounts, yes as I said, these are good against armored shells. For the large weapons it's intentional, and makes perfect sense. But even for the fighter stacks, it's not really a balance problem except perhaps against the AI, which isn't programmed to realize how to counter it.

100 fighters in a stack may be able to dwarf the emissive ability of an armored shell, but it also forces the fighters to fire one giant shot at once. This will be a disadvantage if the enemy has fighters in smaller Groups, because the 100-stack will only be able to fire at one enemy group per turn, wasting any excess firepower, while incoming fire against the stack won't waste any firepower until the very end.

Moreover, as oleg mentioned, small ships remain viable throughout the game - a squadron of smaller ships with lighter weapons can often evade the less accurate big-mounted capital ship weapons.

Which is not to say that every ship should have an armored shell against all opponents. The whole point is that there are choices with trade-offs, and not just "X is better than anything else in all ways", moreso, I think, than in the unmodded game.

As for hulks with only structure remaining, that can certainly happen, tough it's pretty varied how ships take damage, and depends on the armor and the weapons used and, with armored structure, a lot on chance. Usually the armor pretty effectively protects the useful components, but sometimes the components get nailed before armor. Usually it's a mix.

PvK