Unless you are using a mod, upping your capital ship numbers is very expensive indeed. First, you have to buy the research, and then you must drop another 3000 credits. The result is that caps end up costing around 4800 credits plus metal/crystal.
But for the record, don't use them. Late game, they are not used for their SC numbers so much as they are for their SC support abilities. For instance, Repair Cloud vastly improves the survivability of SC. Sure, they might increase your SC numbers a bit, but they are not cost-effective for their SC numbers later in the game.. Capitals, aside from the first 30 minutes, are support ships.