^
Going in tandem with Ventus' explanation, I don't think that he's really upside-down. It's more like he is attached to the ceiling (as the picture seems to designate) and he is reaching downward. In his boredom he'll tap on the drumhead that Link eventually fights on and experiment some new beats. When Link finally faces him, he patters the drum to throw off his aim. As such, since that's all he can do, Bongo Bongo is suspended from the ceiling for his crimes that he committed again Kakariko Village long ago.