That's a good point actually. It's been brought up before and i think aknowledged by the devs as well at one point.
As for attacking ships, it sure does make for some very nice and challenging missions. I don't know what the extend of the ship's damage model complexity will be, but it will be great to be able to damage smaller parts of a ship even when using guns.
I don't expect to sink the Bismarck with just a rack of .303s, but being able to put a couple of exposed AA guns or their crews out of action on a big ship would be cool and make for interesting and varied missions, eg the fighter escort suppressing flak on the target ship so that the slow-movers can get in and hit it properly.
In a similar fashion, it would be just as welcome and quite realistic to be able to sink smaller vessels with gunfire from heavy guns. Armed trawlers might as well be sunk by machine gun fire alone, same for freighters carrying sensitive cargo as long as they could be progressively damaged so that they sink after some time by secondary damage. For example, strafing an unarmored freighter that has ammo containers or fuel drumms on its decks and in its cargo holds.
Finally, and this is visible in some gun camera films floating around, even destroyers could be sunk by concentrated gunfire and a bit of luck, or just by cannon armed aircraft using a combination of the on-board armament and bombs/rockets. I think a flight of mosquitos with their battery of 20mm cannons, rockets or even the 57mm cannon on the tsetse variant would have little trouble in severely damaging or even sinking smaller warships.
Short version: Guns have almost no effect at all on ships in IL2, it would be welcome if this could be changed in SoW
