As there is nothing explicit in the entity files for each Capital Ship about Capital Ship slots, but there is for normal fleet cap, its entirely likely that the game merely counts how many "CapitalShip" entities you have control over and compares it against the CapitalShipMaxSlots count you have from research.

Ie you cant make capital ships not take up any capital ship slots

granted thats from a quick look, if you find a way of doing it feel free to share.

You could always change the crew research options to give yourself effectively unlimited crew slots.