Not so sure. The relations between mafia and unions seems to me unique to the US, or at least not so widespread.
Unions can indeed have issues (on one end corrupt leadership that just pads their bank accounts or screws those that they're supposed to represent, on the other end over-privileging of a certain field), but turning into "unlabelled mafia" is not a core trait.
Certainly it's possible, and yet I don't think there is much other way for employees to achieve any sort of political power over their employers. It's also probably worth mentioning, since we're talking about Japan, the extent to which the worlds of Japanese business and Japanese organized crime are intertwined.
