So here's the thing.

[hardlyboy]

Naoto is biologically female, but she's not entirely comfortable with her gender. If your character mentions to her that they can tell she's a woman, she'll be particularly embarrassed, but she won't tell you to hush up about it. She prefers to be perceived as a detective before a woman, but has come to the point where she can accept herself for who she is to some degree. So touching on her gender is a tender subject, and one she will definitely not be as forthcoming about as, say, Maora, but it's not entirely set in stone and Naoto is still in the process of finding herself.

As a side note, I'll be interchanging masculine and feminine pronouns when referring to Naoto, partially because I don't want to spoil this information for the people who haven't played Persona 4 yet, and also because Naoto herself is undecided. (Here, where I've put up a spoiler warning, I'm using the feminine article because that's pretty much how the game does it; effectively, Naoto is a girl in more private settings)

So the question that I'm asking is this -- Will your character be able to recognize that Naoto is female? I know some of the P4 cast has mentioned this about her in passing, and if someone can tell she's a woman she most certainly will want to know. As with Maora, this situation is not one where she'll want you to hush up about it, but it is something she may want your character to approach with some secrecy.