Kusanagi is able to mentally activate a feature of her skintight bodysuit and hair(?!) that renders her mostly invisible. It does not seem to affect her face by default. After her suit has activated, she waves her hand over her face to hide it. We do not see how she activates or deactivates the suit in the first place. She seems to be able to do so at will. Since this is not based on any existing human biological capacity, a manual control mechanism would need some biological or cultural referent. The gesture she uses—covering her face with open-fingered hands—makes the most sense, since even with a hand it means, “I can see you but you can’t see me.”
In the film we see Ghost Hacker using the same technology embedded in a hooded coat he wears. He activates it by pulling the hood over his head. This gesture makes a great deal of physical sense, similar to the face-hiding gesture. Donning a hood would hide your most salient physical identifier, your face, so having it activate the camouflage is a simple synechdochic extension.
The spider tank also features this same technology on its surface, where we learn it is a delicate surface. It is disabled from a rain of glass falling on it.
This tech less than perfect, distorting the background behind it, and occasionally flashing with vigorous physical activity. And of course it cannot hide the effects that the wearer is creating in the environment, as we see with splashes the water and citizens in a crowd being bumped aside.
Since this imperfection runs counter to the wearer’s goal, I’d design a silent, perhaps haptic feedback, to let the wearer know when they’re moving too fast for the suit’s processors to keep up, as a reinforcement to whatever visual effects they themselves are seeing.
UPDATE: When this was originally posted, I used the incorrect concept “metonym” to describe these gestures. The correct term is “synechdoche” and the post has been updated to reflect that.