I think that Heavy CM Droppers use cargo space. That could be it. I know a lot of other capital ship equipment does when it isn't equipped. But seeing that I don't own any ships that can make proper use of a Heavy CM, I can't go check... sorry. Try buying one, then unmount it. See what it does to your cargo hold.
It won't take that cargo when you mount it, so don't be afraid to use it on a ship that have enough energy to use it. It takes a HUGE chunk of energy when used, therefore it's useless for fighters, freighters and bombers. Transports can use it, but the energy affects them noticeably, capital ships are fine.