Well first, the "N" part of the prefix needs to be changed, after all Section 31 is not the "Navy". Honestly, I wouldn't give the ship identifying features like that, just in case some part of the stealth system breaks down the ship could not be traced back to the Federation.
Number Id theories (to the best of my memory)
NX = Navy experiment
NCC = Navy Contract/Commissioned
NAR = Navy Auxiliary (?)
Basically if it starts with a 'N' it is related to Starfleet.
Phoenix...
"I'm not saying there should be capital punishment for stupidity,
but maybe we should just remove all the safety lables and let nature take it's course"
"A Place For Everything & Nothing In It's Place"