Because space/volume and not weight is used as the limiting factor?Why not give spacecraft wings, and attach missiles externally to pylons? Or instead of missiles, gun packs?
Space can always be found.
With the current system you determine the maximum tonnage of ship, which means space/volume with 1t = 14m3. Everything that uses up tonnage has to be subtracted from this maximum. You can put things, that use up tonnage, outside the hull of course, effectively decreasing the size of the hull accordingly, as long as the overall maximum tonnage stays the same.
In regards to weapons other limits exits, such as Hard-/Firmpoints, which in turn determine the number of fixed mounts, turrets, etc. Is this limit too restricting in the current system?