Look at the ships that we've seen use the NX- prefix: NX-01 Enterprise, NX-2000 Excelsior, and NX-whatever Defiant. Each of these ships are revolutionary prototypes/proof-of-concept vessels.
As soon as the transwarp program ended, the Excelsior was given a standard NCC registry. IIRC, the ships of the Defiant-class also use NCC registries. It's quite possible that the NX program will probably remain so until after the formation of the Federation.
Now, while the 4-nacelle design of the Constellation is certainly innovative in 2284, is it such a revolutionary concept that it warrants an NX designation? Personally, I'd say no.
Davy Jones
"Frightened? My dear, you are looking at a man who has laughed in the face of death, sneered at doom, and chuckled at catastrophe! I was petrified."
-- The Wizard of Oz