There's two ways to protect your external assets - and I love this about the game, it's creative. 1: Bury them. 2: Put them on long stalks that are difficult to hit accurately. You can partially bury your components, especially guns can be linked to a Gun Control to angle them, and then remove the controller, resulting in a permanently diagonal gun which can be linked to a regular control box. It's better shooting because you can shoot out of a diagonal easier than the enemy can shoot in. You can also leave your guns in their default orientation but nestle them "volcano style" to provide protection from angles shots - they'd have to shoot straight down your own barrel to hit the gun directly, or blast their way through armor.
The alternative is to put your guns on long stalks. This makes them more difficult to hit because they rotate more quickly when the ship turns, and presents a smaller target than your broadside. This can be countered by block-shots though, an array of anti-personnel guns that fire in the same direction can throw a "laser net" and more likely hit it, although they'd do little damage. You also have to deal with power needs, either setting the reactor at the gun or to run armored wire. On the plus side, when you get a camera positioned there you've got a really wide arc of fire, so you can have fewer guns than a broadside ship and still be able to hit targets that aren't on your broadside.
Damn, multiplayer fights are gonna be intense!