Plus just cause the highest NCC we saw was 2000 doesn't mean that is the highest number in-universe. Nor do we even know if the registry number corresponds to the number of ships in the fleet.
It does not, and never has. the Registry numbers are (usually) based around classes, at least they were anyway. Later on they seemed to chuck that directly out of the window. Guess in the D. Moore era they just got too lazy to follow logical patterns in the registration system for the various classes and just started pasting random numbers on the hulls.
I do like in the Titan series they at least tried to bring it back into order with the Luna class registrations, but sadly it was too little too late.