(If your answer is 'because the manga does it', then I'll just convert my question about the anime to a question about the manga.) In both sub and dub, what I recall is that the narrator calls Kaguya by 1st name but pretty much everyone else by last name. You can see for yourself besides the regular narration, there's also the official result at the end of a sub-episode.
Some examples from s1 and s2:
1 - Shirogane instead of Miyuki (eg S02E03)
2 - Fujiwara instead of Chika (eg S02E02)
3 - Ishigami instead of Yu (eg S01E06)
4 - Hayasaka instead of Ai (eg S02E04)
5 - Kei Shirogane instead of...well I think this 1 is ok since Kei is not a major character or at least has the same last name as a more major character (specifically a main character). (eg S01E08)
6 - Iino instead of Miko (eg S02E09)
Kaguya instead of Shinomiya (eg S01E01)
Edit 1: Guess: Wait...I think easy guess...far easier than the (cw) answer I posted. Kaguya is simply the viewpoint character and so is called by 1st name.
It's like Harry Potter: Iirc, JK Rowling's narrator calls Harry Potter as Harry and calls the rest of the characters the way Harry would call them except possibly for the title/honorific.
- Eg Harry calls Ron Weasley as 'Ron', so the narrator says 'Ron'. Eg However, Harry calls Severus Snape as (Professor) Snape, so the narrator says 'Snape'. However, if Harry calls Severus Snape as (Professor) Severus, then I guess the narrator would say 'Severus'.
But eh could be double entendre. Like both viewpoint character and something in my cw answer.
Edit 2: Btw, in the afterword in Volume 22 Chapter 221.1, Aka Akasaka actually refers to Miyuki Shirogane by last name but to Kaguya Shinomiya by 1st name.