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.