Japan's farmers are old because Japan is a segregated society. Farmers, fishermen, and other manual laborers who's professions are considered 'unclean' are a subclass heavily discriminated against.
No. You're confusing manual labour - well respected, fishermen and farmers especially - with "burakumin", the old class of people that did work forbidden by buddhism, such as butchering, leather tanning and so on.
Discrimination of burakumin still exists, but mostly among the kind of people that worry their daughters will marry the "wrong sort" of people, and "wrong sort" also includes not having a foreigner in the family tree, not being a member of the right country clubs, having insufficient money and so on. The recent mayor of Osaka, for instance, is burakumin, but while there are many reasons to dislike him, I've heard of nobody doing so for that reason.