Other than the starship chart in "Court Martial," there was no other use of NCC for an explicitly non-Enterprise
type starship in TOS. As Christopher
points out, though, by TAS they were comfortable showing the freighter Huron
with it. So, it's possible that the intent changed.
We know, of course, in the real world Mr. Jefferies rationale for picking NCC; N meant the USA, and CC represented the Soviet union, so NCC together gave it an international flair.