There are several reasons why no one noticed that Natsume was a girl:

1. She was dressing as a boy, therefore no one should suspect her.
2. On the novel, an onmyouji can identify whether you're a girl or boy based on your aura. Boys naturally have yang aura and girls have yin aura. <br><br>
Normally, when a practitioner has a shikigami, the shikigami's aura should be the opposite so that their compatibility will be in harmony.<br><br>
However, Natsume's prideful shikigami which is Hokuto have a yin aura, therefore it made conflict in their auras, thus negating the yin aura and making it a yang aura. In result, anyone would assume that Natsume was indeed a boy.
3. It is rumored that Natsume was Yakou's reincarnation, since she was the next heir of the Tsuchimikado family, they preconceived that she is a boy.