Well, the Rules are different for women, but this happens pretty often in women's restrooms. It means, "there's no toilet paper"--but we usually accompany the gesture with a "please?"
I certainly wouldn't wave my hand under the stall wall--NOT NOW anyway! (I'm getting paranoid.)
I remember one time in junior high school, when I went in the boys' rest room. A boy, with a desperate look and voice, stuck his head out of a stall and said, "Hey, Buddy. There's no toilet paper in here. Could you get me some?" He meant the entire rest room.
I said, "Sure. I'll get you some." I had to go all the way down stairs, get some, and bring it back to him.
He was grateful.