It is a chaotic mess. Here are some suggestions that I believe would help alleviate this mess:
Zone list sorting. Currently, it is based on distance and direction (I think?). It would be helpful to have other options as well, such as standard alphabetical/numerical sorting.
Zone tabs. This would help identify zones for separate bases and vehicles. At the minimum, differentiate vehicle and land zones.
Zone deletion confirmation. There is no Y/N confirmation and no message of what zones you remove. Accidently hit r while managing your zones? Good luck noticing it, and to what zone.
Zone shaping and adding to existing zones. Say a player would like to have the unsorted zone here. This could be one zone, formed that way or with spots added to it. Instead, the player will have to create 21 individual zones, which will convolute the management window.
You mean the cargo space itself or the zones? I tried naming zones (1, 2, 3, etc) to keep track of them, but it just bundled them up based on direction and distance, so it was still a mess.