Even if the wooden CV decks were suseptiple to taking damage form 30mm cannon rounds, I don't think the Destroyers or Cruisers would be all that effected.
In fact, I'm hopeing that someday we can have AP bombs as well as HE bombs. I often think about the Midway Paradox that the Japanese faced, which likely cost them the battle: Do you load HE bombs to attack the "soft" targets on land? Or do you load AP bombs to hit the "hard" targets (The US Fleet). In Aces High we never have to make that choice, because Ships react to bombs in the same manner as any other object.
Hopefully the addition of Armor to the Gun turrets will be one of a few new additions to the Ship damage model. I know that the focus of AH is on the air war, but as a Pacific War fiend, I can't seperate the Naval and Air Aspects very easily.
-Sik