The example of the GMG and their vanilla lore is pertinent to this matter, so I'll summarise. They managed to defeat a large, lumbering Imperial Rheinland fleet using bomber strikes and basically luring them into space Afghanistan in the form of Sigma-19. Also consider the fact that GMG is probably richer than god, since they were the premier supplier for H-Fuel, on which everything in space flies (until Gallia came along).
Money didn't get them capital ships. They've stuck to their roots.
any of the smaller factions listed by Joe have nowhere near the amount of wealth and economic stranglehold the GMG does and has maintained.
Ideally, any fight of a smaller faction versus a house military (say, Rogues vs Liberty) would follow the same pattern. Rogues have a lot of bombers which they can use in hit and run attacks from myriad asteroid fields. The Lumbering House Fleets can certainly decimate them...if they can find them and catch them. To perform that role, you don't really need capital ships. You just need the barghest. The fact that Rogues shouldn't really be engaging Liberty Navy head on is another topic entirely, but hypothetically if they were to fight...that's how it would go.
I'm not touching the zoner topic in here at all, but I do agree that if you're suddenly looking to size up and delete/add ships to factions according to lore justification rather than just a fun ship to have...all factions should be equally subject to such a consideration.
Then again, capital ships are...for better or worse, one of the charms of this mod and I certainly do feel that arguments for fun and accessibility taking precedence over roleplay apply here.