De acordo com a wikia em Números de registro :
The most famous registry number, of course, is "NCC-1701" of the original USS Enterprise. It was chosen by Matt Jefferies, who was a pilot before joining the Star Trek staff, and based the registry number on 20th century aircraft registration codes. In the early 20th century, the letter "N" indicated a United States origin, and the letter "C" indicated a civilian aircraft. As American craft used NC and Soviet craft used CCCC, Jeffries combined the two as NCC.
His philosophy was, "If we do anything in space, we (Americans and Russians) have to do it together." H states the numbers "1701" stand for the 17th cruiser design, serial number #1. Also, upon choosing the Enterprise's registry number, Jeffries decided that the number should be easily readable, so he was careful to avoid numbers that could be confusing, such as 3, 6 and 8.
Portanto, parece que os números foram baseados em códigos de registro de aeronaves do século XX e as letras são um conglomerado dos códigos de país de origem dos Estados Unidos e da União Soviética.