I’ll have to disagree with the usage of “they” too. It’s not particularly that I want to argue if it’s right or wrong to use it, since certainly you can use anything you want when gender isn’t stated and not choosing either would be objectively not wrong.
But in terms of readability, “they” feels too deliberate, drawing more attention to gender when in the context there is no particular focus on it (I means it’s literally omitted in Japanese since it doesn’t matter and is understood). “He” would seem wrong when they all know it’s a woman, but even so it would have the feel of it just being casual since it was just the way they’ve (or just Nao) always been thinking of each other. That said I’m pretty sure they all have awareness it’s a she now (especially now for Nao HUEHUE) so that would be the simpler choice and wouldn’t be out of place at all.
I do believe the last thing you want to do is to disturb the flow of a very casual friends interaction by the word usage of “they” which gives the feeling of: I’m going to respect their gender choice!!, or just plain drawing attention to the whole gender thing, because the whole deliberately giving consideration to the gender is not something in the minds of the characters talking at all, since they aren’t even thinking about whether Kou is female, male, or PURPOSELY going with neutral (as is the tone of the translation)