Another weird thing about subsystems- why do they always seem to be near the OUTSIDE of the hull, right where all the fighters can get to it?
Lets face it, only realistic scifi ship design is a Borg cube. All others are full of wings, spikes, towers and such. That not only are complete waste of materials and structurally weak, but also make the ship look bigger than they really are. They usually look nice though...
Anyway. When examinig FS ships, the actual useable space inside the ship is quite narrow (rest being those spikes and wings). There is also the thick hull, or "armour", that protects the ship from harm. And it also protects the crew from all the radiation that space has, so the crew shouldn't be anywhere near the outside of the hull where they will die. So there simply isn't space to place those vital systems in to the interiors of the ship.
It is also possible that the actual systems are tucked inside a closet somewhere in the core of the ship, but something vital is in a voulnerable place (the sensors need something to "sense" trought).