On a related note, if you decide to make only standard variant bays available, don't make them too expensive because noone who doesn't cheat will use them. When I didn't cheat and didn't have variants in stock, I never used fighter bays because they were too expensive and it took too long to get the money for them and their fighters. Despite mantas being awesome, replacing the fragile fighters was a nightmare. If you lost a raven's worth of mantas, you were out 6 mill, and it can take an hour of boredom to raise that much by conventional methods. I never used the standard thunderhead bay either, because it was worse in every way than the pirate one, not that I would have used it anyway were the pirate variant not available. In my opinion, it would be best to make the player choose between a set of different yet equally good variants, only able to use one. So if you buy the beam variants pv bay, you can buy more beam variant vipers and bays for them, but you can't buy any for the missile variant, and vice-versa. Let a manticore-equivalent sum of credits be the amount of money one can get from boarding a reasonably challenging foe from a lucrative race. The bays should each cost only one or two manticore-equivalent credits, unless they're manta-awesome, in which case they should cost twice as much as the other bays of the class. The fighters should never cost more than one manticore-equivalent sum each, and in fact should cost much less (usually) in general. If the ships that will be carried in the bay are not fighter class, average the price of the ships with the price of an equivalent fighter, and for the bays, average their prices with equivalent fighter-class bays. Make sure to keep bay mass down and scaled for class and fighter strength, as well.
Sorry for the wall of text, but I hope I've helped.