Two very technical explanations:
1) Sensei's actual words are "...come to think of it, you [Ayane] are
rarely even around when that happens, are you?". It's not really
never if one wants to be a Mr. Literal and if one wants to count
Stop Looking For Answers as Ayane actually being around Sensei's past blackouts at least once (though it was by the very end of it and Ayane at the time didn't know what was happening). Still, I would also assume that "rarely even" is enough the same as "never" to avoid playing around words too much.
2)
TH15 15NT M3 is v0.38 and
Operation: Sleepytime is v0.42, so "technically" by the time of the latter event, Ayane has been made aware of Sensei's strange condition, and can identify it when Sensei was experiencing shit.
Can you elaborate on "morning Ami and night Ami are different in the beach"? am interested.
As for Himawari shapeshifting to Ayane, Himawari has more than once expressed her unwillingness to transform into
her mom; my impression from reset5 is that she does have a valid, existential reason for not doing so and it's not just about preference. So even if Himawari someday starts mass disguising as everyone at every turn, Ayane would still be off limits if there isn't a strong enough reason for her.
(Besides, for narrative reasons, I don't think Himawari pretending to be other girls is, has been, or will be an frequent everyday thing. It's a Pandora's box level plot device if its use is less than meticulous. IMO the transition has to be seen by players' point of view or things get overboard very easily when, technically, she can just be everyone.
You can either believe that Kumon-mi looks something like the following, or this is simply a case of "it makes sense if you don't think about it"