ST precedent was with the Excelsior as NX-2000, experimental vessel. When Excelsior later went into service, we see NCC-2000. Makes sense.
Then we see Enterprise as NX-01, using the NX again to denote experimental vessel. Fair enough, new warp five engine and all that.
But then the Enterprise goes into service for Star Fleet, it should have been become NCC-01. It was no longer serving as an experimental vessel, it was being put into service on missions.
Had the NX-01 refit become reality, I think it would have been interesting if it were re-christened NX-01. http://www.modelermagic.com/?p=26713
I also see what you are saying in that NX-2000 became NCC-2000, but the thing is we do not know how many NX ships were made and how long they were around, canonically. It is very possible a new class of ship replaced them with Warp 6 or better technology, before they could have become an NCC classification.