Nodoka doesn't seem to know anything about Maya, and after Sensei's return where he implies he lost someone, she didn't seem to notice Maya Prime became New Maya:
This also implies that Nodoka has little idea about Niki's relationship with Sensei, and probably nothing about Kaori, etc.
Nodoka seems to see Sensei as an ephebophile, but didn't seem to think he's a pedo:
Which would imply she's unaware of Sensei's pedo "romance" with Maya, and other Wizard related stuff.
Nodoka's lack of omniscience seems to become more and more blatant through out the game. She only recently found out that Sensei fucked Sekai, thanks to Yasu and special notes, but to be fair, she doesn't seem to think Sensei's sex life matters too much outside Kumon-mi/this world:
One world out of billions:
Apparently, based off Nodoka's Chapter 4 'Mille Crepe' Event.
As for Maya Prime, an interesting thing that I don't think has been brought up is the Upside Down Dreams she started to get, around when this timeline started it seems:
This seems related to Futaba's recent TSS which was Upside Down, and quickly became something Futaba thought wasn't real, and struggled to remember. Like a dream.
Maya, Futaba, Noriko, etc, all might be the special kind of gate travelers that Nodoka and Yasu seem to hint at. Yasu also seems to be one, along with Kaori, and maybe a few others, like Ami who Nodoka refers to as a Marsh Warbler:
Nodoka isn't one though, according to her, as they seem to hide from her.
Also:
Bird Nerd Maya is Best Maya.
Maya has likely been Scrawing for millions of years and still never got tired of it, lmao.