Why didn't anyone in the school notice that Natsume is actually a female? In the early episodes of Tokyo Ravens, Natsume is seen wearing a boy's uniform. It is said that this is due to some customs in their family. As quoted from Wikipedia here:


  As a family tradition, she has to present herself as male in front of other onmyouji families, a tradition that was created to hide the true identity of Yakou's reincarnation.


But why didn't anyone notice that she is actually a girl? Everyone except Touji and Harutora who already knew her, assume that she's a boy.
There are several reasons why no one noticed that Natsume was a girl:


She was dressing as a boy, therefore no one should suspect her.
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. 
Normally, when a practitioner has a shikigami, the shikigami's aura should be the opposite so that their compatibility will be in harmony.
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.
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.