I am bumping this back up because I have been reading some more on this case, and it may be that dad wouldn't be in any better position if Japan HAD been a signatory to the Hague Convention.
Apparently the couple was married for 14 years and resided in Japan. The dad is a naturalized Japanese citizen. Although no timeline has been given in the articles, it appears that they had only recently moved to the US, when he cheated on his wife and they got divorced. The children didn't even have US passports.
If they were here less than 2 years (and it sounds like that might be the case) then Japan would have had jurisdiction over any matters regarding the children, under the Hague Convention.
Therefore, the US courts would not have had the right to make child custody decisions if the Hague Convention had applied.
Also, Japan apparently doesn't recognize foreign divorces, therefore they are still legally married in Japan.
While I do still feel very sorry for this father, I am not certain that international law isn't served by the children living in Japan, since that is apparently where they have lived most of their life.
Certainly, if the children were raised in the US, and had only lived in Japan a short time before the couple divorced in Japan, we would be thinking that the father should be able to return the children to the country where they were raised.
Now, of course Japan's custody laws seem to leave something to be desired, but I think that dad would have been on the losing end of this even if the Hague Convention had applied.