From the FJ Tech Manual - NCC = 'Naval Construction Contract'
Exactly. And that's right about the point where the registries ceased to make any sense.
To have the letters denote something as redundant as "Hey, folks, this naval construction contract number here is, you guessed it, a NAVAL CONSTRUCTION CONTRACT NUMBER!" is definitely something Matt Jeffries would never have erred on suggesting. Why, should all automobile registry plates begin with the letters "CRP" just to indicate that this is an Automobile Registry Plate?
FJ messed up quite a few things where the people who actually made TOS would probably have gone for greater diversity and depth of thinking. Giving all types of vessel this identical (and thus completely redundant) three-letter prefix was one of the worst choices there, although admittedly preceded by similarly poor choices in TAS.
Thankfully, some kind of sense of functionality was restored to the registries when TNG and the TOS movies began showing other possible three-letter combinations. And the pattern that emerged seems to establish that NCC means "Starfleet vessel" while other letters denote other kinds of owner or operator.
I really wouldn't have minded more of those N?? things, now that we've had NCC and NX and possibly NAR and then that one offscreen instance of NEE for Starfleet, and all sorts of other N prefices for supposed Federation civilian-commercial ships.
Timo Saloniemi