Most Asian countries are very conservative compared to western ones, especially in public. Going commando is not normal and is quite unheard of.
The problem is not the commando, it's the "what will people say?" part. In Japan being or doing something even slightly different can easily be blown out of proportion and make you the topic of gossip or bullying, because that is the easiest way to build status (which is vital in the heirarchal society of Japan). By putting someone down, you make yourself higher on the hierarchy ladder. I know stories about girls who got bullied for wearing hairpin different in color or design from the rest of the girl's in class.
Seriously? That' f** up...
Kinda stupid, a lot of people go commando, it's no big deal.