I used to have both base space yards and space yard ships in the AI design files include cargo. But the AI was too stupid to remove the units it built from either type of vehicle so it ended up with wasted units that were never used clogging the base space yards and space yard ships.

Have you noticed the AI in Proportions do this? If it's smart enough to actually find the units in the cargo of space yard bases and ships now then I'd keep the cargo space. It's very useful to include the space to hold units you have contructed in the same vehicle.
And I don't think it's unbalancing in itself to have a ship or base able to build and launch units. A BSY with mine/satellite laying bays is an excellent thing to put on a warp point.
