I'm not sure of other cultures, but where I live, dudes don't ask other dudes to go to the toilet together. I'd assume there's such a tendency, at least to a degree, in Japan as well, based on numerous manga and anime. So, I'd say Kanade (Amata) could deduce that Aki (Hanku) doesn't consider them both to be men. So, either Aki is a man willing to escort a woman to the toilets or a woman willing to do it with either another woman or a crossdressing man, which are both probably plausible possibilities. It's not like they would need to enter the same bathroom, after all.