We are playing a game involving warp travel, psychic alien infestations, super-mutating drugs, and somewhat questionable flight physics. I think the issue is less "logic" and real-world rationales as it is balance.
Why do codenames have to take a negligible 1 space? This means that an AU8 Arrow or Hayabusa cannot mount the new LF codes. It was determined before .87 that missiles should take some cargo space - especially with gunboat missile turrets and larger now taking ammo. As many forms of missiles have already had their limits reduced, is it still necessary to add a little bit of cargo space?
These guns take only negligible amounts of cargo space, so will it really shake up the ship's balance? Is it just made to ensure some ships may have to decide between sacrificing codes/turrets to equip heavier armor or haul more cloak fuel/trading cargo? Is it truly meant to be a holdover until a way to figure out how to tie cargo/armor/equipment to a ship's mass? Perhaps an appeal to the balance devs based around these points would make for a better case.