It's not that easy to accept it, even if you have all the evidence of being a lesbian it might take a while to let it sink in since Koto is also the kind of girl that wears a thick mask to blend in.
I wouldn't go as far as saying that she's suicidal, like
@legendaryboya suggested, but she's definitely about to snap at any given moment (She couldn't bear herself to look at Mogumo at the end, prob implying that she's forcing herself to keep the status quo going as a way to keep her sanity)
She's still really struggling a lot because deep down she probably wants to accept Mogumo but at the same time she just doesn't comprehend Mogumo's gender and would gladly accept for them to stick with a binary gender, either female or male, (pref female).
EDIT: I personally think that Koto cannot move forward unless she meets another gay woman like her, possibly in a healthy relationship, so that she can see that the people at the cafe are human beings like her that blend in society and that despite not everyone accepting them (yet), they still can find happiness.
EDIT2: This post is a mess 😔 but I can't help but feel emotional when it comes to this character that really hits me home.