The problem is the all-or-nothing damage model, it means that a hit with a 1600lbs AP bomb on a ship is next to useless since the ship is still fully functional, all you can destroy is a few guns. CV damage heals in 5 mins so your hit will not help others kill the cv either. In real life such hit would most likely force the ship out of the battle or even sink it.
It might not be possible to do but one solution could be to have the flight deck as a separate object that you could destroy w AP bombs and thus make it impossible to launch planes, It could have a 15 min damage like a hangar.