I'm not sure what qualifies as a "secret", so I haven't listed much for now. SPOILERS!!
Sana's biggest and most important secret, in my opinion, is the fact that Kurata Misako is not her biological mother. Sana's biological mother, Sakai Keiko, abandoned her when she was a baby. Keiko was only 14 years old when she gave birth to Sana, and feared what society would think of her. Meanwhile, Misako had found out that her chances of conceiving a child were little to none. Somehow Misako stumbled upon baby Sana, and soon after adopted her.
Misako believed that Sana should know the truth, so she attempted to explain it to Sana when she was quite young. Many argue that Sana was too young, but Misako believed it was for the best. She began to develop a plan to find Sana's biological mother. She enrolled Sana in Komawari (see career), in hopes that she would one day become famous enough to reach her biological mother.
When Sana became famous enough, Misako began to write the book My Daughter and I, describing how she found Sana abadoned as a baby. Her hope was that Sana's biological mother would read the book and come forth. Misako's plan worked perfectly; Sakai Keiko came forth to admit that she was Sana's biological mother.
Another little "secret" occurs only in the manga. Not in the anime! Sana has a condition called "Mannequin's Disease". When Sana was a little girl, for a period of about two weeks, she became expressionless. She didn't smile, she didn't laugh.. nothing. However, poor Sana didn't realize anything was wrong; she felt completely normal. Somehow she managed to snap out of it when she met Naozumi for the first time.
I'm not sure how Naozumi managed to get Sana back to normal, but he did, and that's what matters, yes? Anyway, it turns out that Sana's "condition" was triggered when Misako tried to explain that she was not her real mother. Later on, this condition comes about when Sana learns that Hayama is moving to Los Angeles.