Are there any female mangaka pretending to be a male? Manga magazines are usually targeted to a specific age and gender of readers. Usually shounen manga are written by males even if there are notable examples of female artists working on shounen series (e.g. Rumiko Takahashi, CLAMP).

Are there any case of a female mangaka pretending to be a male using a pen name to adapt to a specific gender or just to challenge her readers and later reveal herself?
I think none.

First of all, in this link, these are the only manga examples created by authors who pretended to be the opposite sex using pen names.


In the anime ef - a tale of memories, Hirono Hiro, 17 year-old male who is a professional mangaka, writes under the pen name Shindou Nagi, claiming to be female. Given that his work is shoujo, it's understandable. 
In Otomen Tachibana Juuta writes sparkly romance shoujo manga under the penname Sachihana Jewel, and refuses to disclose his real identity even though the manga is hugely popular, because he's afraid readers wouldn't take well to their shoujo manga being written by a man. He goes as far as crossdressing whenever he needs to appear as Sachihana.
There's also his (Tachibana Juuta's) favorite mangaka, Mira-sensei (short for "Mirage") who dresses, speaks and behaves like a classic '70s shoujo manga character, for the same reason as Juuta. His motto is "Because we're professionals!"
In Himitsu No Hanazono the four brothers work under one female name to publish their shoujo manga. 


Which all are male mangaka pretending to be female for their shoujo manga. And in this list are female mangaka, and you can notice some created shounen manga. If there are some of them who pretended to be male, then it should have been stated there because it's a must-know.   

Why none?

According here, female mangaka were greatly accepted so I think there is no need for them to use pen names to hide their true identity, either for the reason of having their shounen manga accepted or the reasons you mentioned above. And there exists a lot of female mangaka who created/creating shounen manga.


  Later popular artists include the highly prolific and successful
  Rumiko Takahashi and rising star Akira Amano (both drawing primarily
  shonen stories for boys) as well as the female collective CLAMP.


Furthermore, I think male mangaka receives more discrimination for writing shoujo manga than female mangaka writing shounen manga. It's much like the discrimination when females are okay to hold hands with females (most will think that they are best friends) while males holding hands with males are.. not so acceptable. If you know what I mean. :P

Well, the links I provided might not be complete or I might be wrong (forgive me) so I'll just update this answer if I find something. As of now, this will be my answer.