I live in a fairly unique part of Japan in that there is such a large concentration of foreigners and there's also a lot of mixed marriages. In recent years there's been a huge baby boom. A large portion of people we know have recently had or are expecting a baby. I think there must be something in the water up here!
Still I think there is some truth to that article. Japan doesn't have such an aging population issue for nothing, people just haven't been having enough kids.
It is my experience that in most marriages between Japanese couples up this way the wife will discontinue full time work. And nearly all will discontinue work altogether for at least a few years after having a kid. There still seems to be a reasonable amount of societal expectation that they do this. There also appears to still be some prejudice against advancement for women in the workforce, especially if they are married or have children. So it stands to reason that if women want to have a successful career here getting married isn't really going to be very helpful.
Also with Japanese men still working some of the longest average hours per week it stands to reason they are hardly feeling all that amorous after 12 hours+ at work and probably a few drinks afterwards before getting home very late at night. From what I can tell from discussions with friends it's also not all that uncommon for husband and wife to sleep in separate beds or bedrooms.
Government assistance for families is minimal, certainly not enough to encourage any major baby boom in recent years. When a fair portion of wives also drop out of the workforce permanently it doesn't make it any easier financially for couples here to have more than 1 or 2 kids.