Re: NCC = Not Constitution Class?
My speculation on the matter is that MJ was drawing on what he knew about aircraft designations and marrying that to a serial number format. The Flying Fortress could be viewed as the 17th bomber design (B-17) and its variants were appended with letters (B-17G, for example). While I am aware that format is similar but not the same, it is not a stretch by any means to see its influence in what he derived.
Battletech uses a similar system for mechs, with most mechs having a production code that's normally based on their class name (with very rare exceptions), so that the Mercury class battlemech (which became the basis of the Clans' advanced omnimech designs) has a designator of MCY-XXX. Clan mechs notably lack such designators, but sometimes have alternate names given to them by the House troops during the early Clan invasion. Interestingly, most other vehicles lack them as well even though they're prominent with battlemechs. Only class names are used.
"If you think you're brave enough to walk the path of honor, then follow me into the dragon's den."