You're exaggerating. There are only two "explanations," one of which is that she has a name that no one in authority over The Canon ever bothered to nail down, so it's different every time (just like the good old days with Walter Sulu and Penda Uhura), or that she's an alien, her personal name is unpronounceable, and "Number One" doesn't just reflect her rank on the ship, but, coincidentally, her position in the meritocracy of her home planet. I grant you, that's a bit of a stretch, but it does come from Majel Barrett and D.C. Fontana, so I think they're entitled to think of some complicated wackadoodle sci-fi worldbuilding with regard to this TOS character, out of all TOS characters.
Considering the sources, my top preference would be that they go with "Una," implicitly canonizing the Barrett/Fontana backstory, then punting and continuing to just call her "Number One," then just inventing some random name, with my least-preferred option being to pick one of the conventional names she's been given in a book or comic. Using "Una" also has the benefit of not shooting DSC's cross-medium aspirations in the head like a crippled horse over something incredibly petty. "We'll coordinate closely on the novels, and draw on them for backstory, and we'll only contradict them if it's for something really important, or if we want to establish a legacy character's name as our own mark on history."
