WARNING: The following contains major spoilers for both the comics and television show adaptation of The Boys.
By the end of Season 2 of The Boys, the most enigmatic member of the Seven, Black Noir, was left in a coma, and the status of his brain function left ambiguous. This surprise defeat at the hands of Queen Maeve, who used Noir's tree nut allergy to her advantage by force-feeding him an Almond Joy, was significant for many reasons. First, seeing the formidable Black Noir being taken out by a fairly common allergy was a stunning (and slightly comedic) revelation. But this moment also seemingly confirmed that the television show will not be adapting one of the most insane plot twists from the comics: that Black Noir is in fact a clone of Homelander.
So far, Black Noir has remained mysterious, with his zen-like silence juxtaposed with surprising feats of brutality creating many moments of unexpected humor. He has also remained completely masked throughout the show. However, when Queen Maeve pulls up his mask to force-feed him the nut-filled candy bar, the portion of his face that we do see seems to be that of Black Noir's actor Nathan Mitchell, and bears no resemblance to Homelander actor Antony Starr. This revelation apparently confirms that Eric Kripke will not utilize the iconic comics plot; however, according to this Reddit fan theory, Black Noir's television arc might just mirror the comics after all.
The Reddit theory posted by u/MLBPGDSP posits that despite certain subversions and deviations that the television show has made from the comics, that the show is actually a fairly faithful adaptation, and has actually set the stage for many staple moments from the original story. These include the backstory of Mother's Milk, Victoria Neuman/Vic the Veep's rise to political prominence and Hughie gaining superpowers from Compound V. The Redditor also theorizes that the Black Noir "face reveal" was an elaborate bait-and-switch from the writers, and that the Black Noir that comes back in Season 3 may not be the one who went to the hospital in anaphylactic shock, but instead a clone of Homelander.
This theory is promising for a few reasons. First, the OP's other points on the show's partial subversions of the comic source material are spot on – the ending of Season 2 seemed to especially point to MM and Neuman's stories being key plot lines in the next season. It also makes logical sense why Vought would want to swap out a potentially brain-damaged Noir with a Homelander clone.
In the comics, Black Noir was created as a deterrent if Homelander ever went rogue. The potential new Black Noir could be created for the same reason. After all, Stan Edgar and Vought have recently had problems with the increasingly erratic Homelander. In addition to his usual heinous activities, Homelander has had some pretty major screw-ups recently, including him kidnapping his son from custody, intimidating Stan Edgar, killing Vought security forces and to top it all off, hooking up with a literal Nazi. This could once again be the show's writers attempting to throw viewers off the scent of a well-known plot twist by appearing to change the narrative whilst planting the seeds for that twist.
Actor Nathan Mitchell has confirmed Black Noir's Season 3 return, but has also expressed that he would be fine whether or not Black Noir is ultimately unmasked. So although Mitchell will continue playing the masked man, it is possible that the show could still pull off its most ambitious twist.