I propose that everything ie repairs, upgrade mods, cargo etc, go in the hold of the ship (hold space for each ship would need to be looked at) and the separate upgrade area is removed.
Anything in the hold would take up different blocks of hold space depending on how big they are, ie ropes and blocks upgrade would take up less space than extra planking for instance.
I just feel this would be a step in the right direction and is reflecting what happened in real life.