I might be a little late to the discussion, but yes, Naoya has already discovered that Kou-kun is a girl (as seen in chapter 30), which led to some drama. Kensuke and Yoshiki had always known this (as shown in the last panel of chapter 20) because they were in the same class as her, and they even made fun of Naoya for being oblivious to it. In chapter 52, they bring up the topic of how they should address Sakuragi now that everyone knows she's a girl. Naoya attempted to start calling her "Kou-chan," but that nickname didn't catch on, so they continue to use "Kou-kun" instead.