Yeah, that's an extreme example, but the trains there are regularly packed cheek to jowl (or other anatomical parts) at rush hour. And, it's not like they are hours apart; another one will come along in about a minute and it's the same. Not for the claustrophobic.
Still, Japan is really worth seeing if you get the chance. I wouldn't rule it out just because you might get asphyxiated or some silly little problem like that. The locals survive, and you will too, probably.