Think it's meant to signify slovenly personal habits, which, for the Japanese, is probably considered only a short hop away from the wholesale abandonment of one's humanity. I'm pretty sure I've seen it used before as a character cue, anyway.
Vezon_The_Insane said: also lol at Reimu scratching her butt.
rainday said: ... Why is Reimu always scratching when I see her?
These comments seem vaguely similar to all the reactions about Sakuya's makeup, people can't help but wonder about it until the great revelation. Gotta say uni mate is simply brilliant in that manner.