^Yes, I get all that. But that hypothesis is only based on the idea that the Kelvin's registry was some sort of basis for four-digit registries starting with 0001 and working their way up to 1000. But the existence of such ships as the Grissom (NCC-638) do not support this. It would therefore make more sense to hypothesize that sometime during construction of ships with four-digit registries under 1000, Starfleet simply decided to omit the leading zeroes from certain vessels.
No, that's not what it means. It means it was previously a 3 digit registry number (100 - 999), and they ran out of numbers, so they switched to 4 digit and added the Zero to the ones still active.
Let's say we started with NX-01 and thought NX-99 would last forever. Then something happened to change it from NX to NCC, and they used enough of 01 - 99, that they figured, might as well make NCC start with 100 and go to 999, that'll last us forever. (And the 20 NX-xx still in Service, we'll call NCC-100 through NCC-119 or we'll add a leading Zero to their original numbers)
Then more ships were assigned Registry Numbers then they imagined and they decided to switch up to 4 digits and the 50 or so NCC-100 through NCC-999 still in use had a Leading Zero added, when they started newly built ships at NCC-1000