And yet, historically, they were around in Japan. When the lord of the castle wasn't present it was his wife who was responsible for making sure the place ran smoothly and was properly garrisoned, even having her own cadre of female retainers to help her. Similarly, female ninja were quite present, and while they did prefer disguises and the honey pot for obvious reasons, they still knew how to sneak around and if necessary defend themselves.
Of course, this being Ubisoft we can't have actual interesting, fun things. We will not get titties, we will not get an attractive tomboy ninja, we will get an uggo in a burqa and we will be expected to like it.