Might be a ship would be able to damage a stack like in Civ 3, I think you mean attacking a stack right, without engaging it. Only you would make that damage really cap very soon at like 80% maybe a bit more for a battleship. However that would also be possible with an ironclad, ship of the line, frigate, anything with long range offensive cannons.
Another option would be allowing ships next to a city to automatically bombard them if hostile and then start damaging units in them, per one...?
If you do plan to make ships able to attack cities and get destroyed or retreat like catapults, cannons etc. You like have to give them negatives, from moving close to a coast risking to be fired upon...
Coastals forts would also be a plausible next step, to reduce bombard damage, and raise then defence against ships. It would mean you got to add a load. Also you shouldn't be able to bombard away the coastal defence...