*Very* few people commute on the shinkansen in Japan, and the distances you're talking about would run around $200 USD per day. I can't think of a single person I knew during my 10 years living in the country who commuted on the shinkansen. If such a commute became necessary a company would just foot the bill for a small apartment and relocate the employee.
Commuting by car is what is actually rare in Japan. In such an urbanized country, with such a robust public transport system, nearly everyone takes the train, or the subway, or the bus. Only in the boondocks do you find the majority of people commuting by car.
Two hour commutes on NORMAL trains, however, are not rare.