Yup, they have different specifications and new designations (they're all listed in the Prophecy Gold manual.)
The only major difference here seems to be giving up some offensive punch in exchange for speed. The exception to this is the Vampire, which got almost a 100 CM increase in it's shield rating, and the Piranha (Which, interestingly enough is listed as a C variant, instead of a B variant as the others are) which got a significant change to it's gun's load out (which I think was peoples primary complaint about the ship).
What's interesting is that on ships that gave up a varied weapons load out for Ion Cannons, the Gun Power rating doesn't change but the speed increases.
The only conclusion that I can draw from these changes is that Confed wanted to do the following:
1) Simplify the large amount of guns and weapons across every ship for a more standerized loadout. (This fits with Confeds "peace-time" navy philosophy of building 10 big carriers instead of 40 smaller ones)
2) Increase the speed of all the fighters across the board. (This is the one stat that is changed on every ship. And I have to say, after abusing my afterburner so badly to chase down Nephilim skates and stingrays coming after my carrier, this makes a good deal of sense. And that's to say nothing of chasing down Squid fighters.)
3) Increase the offensive capability of the light fighter so it is better able to handle combat situations. (This seems to be the biggest change of all, and I think it would be safe to infer from the C designation on the WCSO Piranha that there was another "lesser" variant in there somewhere that was probably a test run in preparation for upgrading the ship to the more "final" C Version.)
What I find most interesting about all of these combined changes is that it seems Confed is altering the tactical load out of it's fighter wings in a way that leans towards a more offensive capably force. Given that at the end of WCP the Alien Threat is supposed to be Eliminated (And believed to be so again at the end of WCSO) this seems to be a very odd move indeed.