Well, I can see where there misconception for it can come about, but Nintendo in general is pretty good at creating systems, games, etc. for all genders. Whenever I shop around for games for my 3DS I mostly find games that aren't geared towards a specific gender, but are inclusive to everyone.
Sure, there are some simulator games out there that are arguably female-focused, but those sort of games aren't necessarily hard to belt out. There are also more games out there for younger children, which is what some of those games are made for rather than a specific gender. However, typically girls and boys grow more drastically different once they reach double digits, then they merge again once they reach adulthood. This doesn't fit for everyone, but the gap for games strictly for male or female is usually the ones made for preteens and teens. For those you will see a very stark difference.
However, with Nintendo systems in general, as previously stated, they are really good at creating games for everyone. Even games where one gender may seem to be the focus is still balanced enough to where the opposite gender may want to play.
Now, if you were asking about app games for phones, Facebook, etc. then I would definitely say those are female oriented. Statistically, last I checked, the buyers for those are middle aged women. 3DS is all ages and all genders.