A maid who works and lives in the Scarlet Devil Mansion. She does a maid's duty perfectly: cooking, cleaning, washing, babysitting, knife throwing, etc. — Sakuya Izayoi's Profile from Immaterial and Missing Power
Sayoko Shinozaki from Code Geass, whose true badassitude is revealed mid-second season. There was a semi-serious fan theory in the first season that the main character's maid was secretly a ninja, and the series creators liked the idea enough to make it canon.
Technically denied by herself. When Rolo calls her a ninja, she corrects him, and calls herself an SP - a reference to Japan's Police division dedicated to bodyguard duties, itself heavily based on the American Secret Service. Of course, she just happens to have weapons similar to those a ninja would use.
An episode of Ghost in the Shell featured a reclusive billionaire (who later turned out to be Dead All Along) with a mansion staffed by gynoid maids with hidden guns that flipped out of their arms. They went down like chumps, though.
Fiore from Chrono Crusade doesn't actually know kung fu... but she is a superpowered jewel witch capable of summoning giant crystalline killing machines, so I think she counts.
Rosarita Cisneros aka Roberta from Black Lagoon, who isn't as much a Ninja Maid, as she is a Terminator Maid. She doesn't just know kung fu — she's bloody invincible, not to mention carrying enough weaponry in her maid uniform to depopulate a small country. considering that she used to be the infamous "Bloodhound of Florencia", the most dangerous hitwoman from the FARC...
Ditto her younger apprentice and fellow Ninja Maid, Fabiola Iglesias.
It's heavily implied that the agency member Mori Sonou from The Melancholy of Haruhi Suzumiya is one of these. Though technically she only pretends to be a maid as part of her cover.
She demonstrates her true badass colors in Haruhi-chan but considering the series' status...
Hanaukyo Maid Tai. Pretty literal in the case of Konoe, a Comically Serious ninja maid and Taro's personal bodyguard, and Yashima Sana, Konoe's lieutenant.
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