I am not 100% sure but, I do not think the skirts, being short, is compulsory at all, but quite the opposite (i.e. they are longer, but the girls do not like them that way) Skirts of younger girls are usually below the knee, it's only when they get 15 or so that it magically "shrinks". They are still longer than you can see in the streets, girls just fold them over and over to shorten them.

I asked a friend (Japanese, girl) how come they are not even wearing panties when it is cold or something. According to her, girls are not allowed to wear colored ones (which includes black), and skin-tone ones are perceived to be a thing of old ladies.