@Nuerlia If I had to guess, it would most likely have to be two obvious things, her face and her actions i.e. her movement for example. While in current-day Japan, there are many Japanese who can pull a girl look but are still guys (TRAPS). They do this with help of camera effects, photoshop, and most importantly makeup. Here in Edo period Japan, if my memory serves me correctly, makeup was not available to many as it had to have been expensive and was used usually by wives of nobles and such. So here, Shizuko does have a feminine face and has no current need for it as we've seen so far. With her facial proportions, you would probably be like those army guys and see she is a woman or at least looks like it. It may be hard for foreigners like me to differentiate between male and female Asians as some have real androgynous faces but Shizuko does not here and as such, her face gives her away the most. Now for more the trained eye, Shizuko's body actions could also act as a sign of her being a woman. Remember women walk with their elbows more inward toward their body while for men, their elbows point outward away from the body. So if someone carefully looks, they could prob tell Shizuko is a woman by the way she walks.
That's just my take. As you said, her face is the real only dead giveaway.