After reading over that article I could see some justification for interesting ship prefixes based on ship class.
The Raven and SS Vico for example were both research vessels and both used the NAR prefix. Although not starfleet designations I could see people using something similar in a RP role. I could see a justification behind starfleet pressing into service a former research vessel, or a former independent human research vessel joining star fleets ranks in a temporary basis in defense of some planet.
With the new Vulcan and Andorian ships to hit the game shortly I could see unconventional registry prefix's added to the game for these non starfleet built ships.
Im pretty much ok with anything as long as there is a plausible explanation of why its there or what function it serves.
I can't seem to find any reference to Starfleet vessels having either NCX or EX, closest I could find is ECS, meaning Earth Cargo Ship, hardly fitting for a war/exploration ship. I also cannot find any reference to the Aeon (Future's End) being NCX, most seem to agree it is registered under UTS. The Relativity (another time ship) was NCV-474439-G, but that isn't something we would likely see in 25th century Starfleet, there not being any time ships as such. NAR is used, but only on civilian vessels, might come in handy if they ever put in a non-aligned faction.
Apart from the canon NX (experimental) and NCC there is NXP, but that is a pathfinder vessel, or proof-of-concept ship for some new technology, and never intended for actual use. There are several other canon registry letters, such as NSP for the Vulcan merchant fleet, but really, I can't see just slapping on some random letters just for the heck of it.
Okay, so there is one ship in another video game (a crappy one at that) with the aforementioned prefix. Funny it doesn't show up in the lists on Memory Alpha and Beta. Why are you interested in these particular ones, and what do they even mean?
as you may have not noticed as well... NX-01 is in game already and it's soft canon too you might well have to take the fact NX-01 is diffrent from rest of other ships and it is soft canon plus hard canon
Yeah, best case that can be made for any of these is ISS, and honestly, I personally would prefer not to have them in game. I have enough problems with the ragtag freedom fighters of Smiley transforming into a cutting edge conquering military who can suddenly transport entire fleets into another reality within a few decades. I mean, even taking the huge leap to them reverting to their evil ways they could hardly afford to send entire fleets into another reality when at least the Klingons are still around in their own, not to forget the Bajorans, Romulans, Breen, et. all.
That said, I would support ISS in game, since we already have the uniforms and such, since nothing will force me to use them. I can't say the same for the rest of these quasi-soft canon and barely mentioned prefixes.