Reloading a tube from the cargo hold would be done by a robotic arm, and a rail system like any modern submarine. I mean, you can jettison a specific type of cargo from your hold, so there is allready some way to manipulate individual cargo crates.

If rocket ammo goes in the cargo hold, the tubes shoud be tuned so that the current 4cu fighters can't take more rockets then they currently can, or maybe a bit less.