Yay! Decks! Hatches!
Decks and hatches should be paint-able and armor-able, that's all. (Could use different sprites, "Wooden Armor" could use the sprites that's implemented now, and "Wood Wall" could just be a railing. "Reinforced wooden armor" could look like a sturdier version of the Wooden Armor.) For balance sake, it wouldn't protect crewmen any better (or very slightly), but the decks wouldn't get blown up as easily.
Aside from giving hatches more armor and hp, making hatches armor-able would let people blend them into their ship better if they wanted too.
Decks can't have armor? Oh, wow. "Shoot here guys! This is the weakest part of the ship!!"