Can't you, like, spend half an hour switching half the ships' main weapons out and changing the hull colors a bit? We could be talking in-game counter tutorials, if a fleet of ships had say a bunch of ion or something, and players interacted with them for long enough to pair 2 and 2 together. It can also increase replay-ability and depth, as having sub-variants means that players could pick and choose what they would bring to a fight based on what the enemy had. The only problem would be if it conflicted with the theme of a faction, a missile only faction shouldn't be messing around with high-power cannons.
SalvagerCorvette- SalvagerCorvette_(Beam/Cannon/Missile)_(Beam/Cannon/Missile/Pulse)_(Effect)
As for extra ships besides that, add stuff like extra armor plates. Thruster boosters. Cargo Pods. The theme can stay the same, but individual ships BPs could have smaller changes that would vastly increase the "Oh wow look a new ship" feel.
An extra thing that would be good is if there was an alamac or something of the sort, that had all of the factions and all of the ships you had seen on the nav screen. This would be great for lore or background knowledge, as you could get a bit more info on that one new design you saw. It doesn't have to be straight stats and a BP, it could be a picture with a bit of lore about it like "Modified variant of the Endurance class Corvette with extra engine plating."
You could even add a backstory, like: "As a response to the Yun Kun piracy attacks, the Trade Federation declared a new mandate to prevent sublight drive blowout, and thus improve effectiveness against the new pirate strategies targeting the vulnerable engines of our Endurance ships." < and maybe have the regular Endurance class have really weak engine armor, and the engine being where the JD is held or something. Hidden design flaws.
Endurance is an example, btw. To lazy to scroll up a bit and find a real ship.