Currently, the Manticore, Constellation, and Hercules are unable to reach their theoretical maximum cargo capacity. I don't know what that stat represents, if not the ability to install more cargo bays in that space. Also, if the player might at some point be able to pilot larger freighters and capital ships, it would make sense for those ships to have multiple bays.
This seems unlikely to cause balance issues, since cargo bays are about the least powerful use for device slots. Still, it would sometimes be convenient to have more cargo capacity and/or get the special benefits of multiple bays.
If you're dead set against this, then I recommend at least adding a higher level cargo bay that adds at least 150 tons to help the Manticore and Hercules and changing the description of the Constellation to indicate it can't be expanded.
I'd recommend permitting this only for the Constellation. It's in need of an edge over the EI500 and Sapphire anyways, and right now its sole advantage can be bought for a trivial amount of credits in midgame.
The Manticore doesn't really need a bigger cargo bay - it does fine as it is, and the 6 segments mesh with its gimmick well enough that it's a respectable ship.