Why? Well, the Retrofit Nebula and Excelsior both have 9 console slots, and their own special ability. The retrofit Galaxy, Intrepid and Defiant classes each have an ability too but only 8 console slots. I don't see their abilities to be objectively "better" than the Excelsior and Nebula (for example, I use transwarp in the Excelsior a lot more often than I use saucer separation in the Galaxy), so I don't see why they have to give up a console.
The other main difference is that you cannot get a retrofit Excelsior or Nebula with a token upon levelling up. But neither is the C-Store the only way to get those ships. You can get all retrofit ships by exchanging ingame currency (Emblems, etc). Since all of them are attainable to everyone just by playing the game, there's no reason to make them unbalanced.
I think the retrofit Galaxy/Intrepid/Defiant should each get an extra console in line with their strengths.
Edit: Wait a second, the Retrofit Nebula has only 8 consoles too? Okay, then that needs a 4th science console. Or the Retrofit Excelsior needs a nerf: It should lose a science console instead.
The Nebula has 8 (3 Science, 3 Engineering, 2 Tactical) and the Excelsior doesn't have a special ability that can be used in combat.
I edited to reflect that before you posted. Still, the Excelsior's out of combat abillty is insanely useful (Especially to those who have not ranked up to Ambassador or do not wish to). Of course no one can have an objective opinion of whether it's more useful than the Nebula's detection grid or the Defiant's cloak. Subjectively I think it is far more useful because it allows you to travel very quickly and have more time enjoying the content which would have otherwise been spent warping around.
I think the Excelsior could stand to lose a science console slot in the name of balance.