If you use Zone to select a region in the editor and Mask, only the selected region will be visible, allowing you to build an interior to your ship.
Your right the hull will be the armour between your characters and space and enemy attacks. Crew space and Console will provide basic protection to space, but not from attacks. Shields can also be used, so in theory you could just use a shield generator.
Currently the system does not check for gaps in your ships design, although it would be fun if people built a disconnected ship and when they flew it the engine(s) shot away!