Destroyable parts on super units sounds like a good idea to me. I have seen this done with a number of units in Total Annihilation mods (3rd party units) though not most implementations there could use work (I think there was a battleship that had its main turrets destroyable, but logically that would be the one of the best protected parts of the ship; also a really old unit was a lighting k-bot that had to deploy a gun, and if shot while deployed the gun broke).

But say for instance there is some super battleship in the naval unit expansion, and it has dual purpose guns and anti-aircraft guns/missiles as well as its big guns. The smaller guns could be taken out easily rendering the ship easily swamped by small unit (like fast missile boats) and aircraft. The big guns would have a low train rate as to make them hard to use in close combat.

Or you could go for a “soft kill” option, where sensors and communications could be damaged. What this could do in the game is hard to tell but maybe reduce accuracy of weapons, or make it have a delay from when ordered to taking action.