I dont know about you but from now on for me ill go with the smaller the size of the ship the better odds you have for not getting a hit registered to your ship. To h_ll with how good the looks of your ship get with higher tiers.
Does the Surface area of a ship affect enemy fire hitting it?
I don't think it does, for 3 reasons. 1) All the ships of the same lineage have the same base ship model, the only thing different is the extra stuff tacked on - for balancing purposes it wouldn't make sense for them to make a larger hitbox. 2) Most ammunition like torpedoes and stuff register hits in a small area rather than being pinpoint accurate like in an FPS. And honestly, if someone is targeting you as long as their aim isn't complete shyte the extra width shouldn't count for much anyway particularly because 3) most targeting is defaulted to have aim assist.
All that being said, I'd be open to testing this sometime if you'd like. I've also wondered about this, particularly with ships that have large forecastles or bridge towers.