nuq is a question word. It is ALWAYS a question. Perhaps the question is rhetorical (asked for effect rather than seeking a response), but it is always an actual question. It should never be used as a relative pronoun like in, "That's what he said," or "I know what that is." The -bogh suffix can often be used for that type of thing.
The verbal -'a' suffix turns a statement into a yes/no question. It is NOT equivalent to a question mark. It should never be used with question words.
nuqjatlh is a special word that is classified as an exclamation. It stands on its own with no other words. Think of it as a one-word question that cannot be made part of any other sentence. While you can analyze it as nuq + jatlh, its components do not grammatically come from What did you say? It's more like Say what?
Would "nuq Dajatlh" not be a better choice here? I always thought that nuqjatlh is less polite but here it seems as though it is a normal question. Now I know that the prefix can be left out sometimes but I'd like to know if that is something that people do who are not in the military.
nuq Dajatlh is fine here and should have been in the accepted translations. I have added it now, but such additions sometimes take more than a week to go live in all the platforms.
As for whether it is a better choice, I would put it as an equal choice instead. nuqjatlh is an exclamation and equivalent to an English speaker saying just "What?" or even "Say what?" (as David suggests above). It's not any less polite than the full grammatical sentence, though I suppose it might not be appropriate for very formal occasions. And it's certainly not limited to the military.