Here is a basic level 2 Pirate Hall base design. Pirate hall and resource storages in the center; gun tower protects the cannons, and cannons protect the majority of the other buildings. If you push the buildings out much more, the cannons won't be able to cover them.
Hmm, you have nice canon coverage, but you're wasting the bidirectional shot of your ship. You'd be better off putting some stuff on the other side of the ship too.
Well, I agree that I'm wasting half of my pirate ship's offensive ability; however, the level 1 pirate ship's damage is pretty weak. When I have more buildings and a better ship I think I will start putting buildings on both sides of the ship.