I think you can imagine the starship production facility also having a large production facility in orbit around the planet for the large capital ships.
Also, economic starbases do get extra revenue from ALL trade routes that pass through thier influence if you add the trading modules onto them (there are 3, you get the ability to build one with every part of the trade tree). You can think of these stabases as a kind of, refueling/rest/service stations that all frieghters stop by.
I personally think they're fine as they are.