A couple things I can think of...
I know Urglub made supply depots that give out a certain amount of 'health', and then stop. So a ship that repairs itself a little bit..or:
You could change what damage the plane bombs do to ships. This is probably the best way.
Is it for your coral sea mod? One thing I was thinking of on that was that the new carriers are super-strong; if you spawn the regular carriers (like you did), they're weaker.
EDIT: Ok, I just wanted to check. I'm not sure what to do here if its for your coral sea:
The problem: The Hornet/Hiryu have DOUBLE the hit points of the Enterprise/Shokaku (1200 vs 600).
The base material of these ships in objects.rfa is 55. I opened the enterprise in Gmax, and it looks like material 66 is for the deck..and lots of others for the sides/whatever.
I was going to suggest changing the material of the ship, and then making bombs do less damage to that material. BUT...that wouldn't work, since the ship has many materials.
The health bubble that gives health very very very slowly to the old ships might be the best?