1) because the Ganymede doesn't have any so that's like the precedence Volition created, and
2) because its main purpose is to build ships, so all of its facilities, energy, room, etc is devoted to that...
3) and you could also say that, like (most) cargo containers, these things aren't supposed to be on the front lines and are meant to be deep inside your home territory where you never (or so you hope) get attacked.
But then again... it's all just a game/fiction so if you make up a valid reason for why the culture would arm their shipyards, then you could arm them.
Joe.