The exact location of weaponry isn't currently represented, I was mostly concerned with getting a sense of the general space of the ship. I would imagine weapon systems to be there around every two to three decks or so. This ship is armed, but not armed to the teeth. The potential locations of weapon systems looks something like the image below. Per deck there are probably at most four weapons systems, but their locations vary.

Missile systems are largely internal, other systems (such as energy weapons) are largely external. Direct connections between the outside hull and the inside would be minimized, so that there aren't obvious holes in the armor. Particularly in the case of turrets this means they are more vulnerable to being destroyed by enemy fire, but if they are there is minimal chance of the hull and/or vital systems being compromised.