I have always wondered this.
In Ent it seems there is 1 and later 2 long range ships and a dozen or so short range vessels like the intrepid. As far as registration numbers go we see NX-01 and 02. Yet there are otherships that were built before hand like as I said the intrepid (what would their reg number be?)
My understanding with Enterprise is that each starship class had its own registry label. Since the Enterprise and Columbia were NX class, their registries were NX-01, NX-02. The other ships would have registries based on their class. EG, I think popular fan conjecture makes the Intrepid NY-01 or something.
EDIT: Although I don't know where I got that from. I just did a quick check on some other sites, and the only thing I can come up with is the Sarajevo from the episode Daedalus had the registry NC-27 in its design sketches.