I do not have an answer but I am curious as well. I know it used to be in old days, I am talking about 20 to 30 years ago it was based on a passport. Japanese passport holders went through “Nihonjin” line and non-Japanese passport holders went to “Gaikokujin” line, did not matter family members traveling together, married couple together, etc.
But time has passed since and looks as there was no official announcement concerning how family members with mixed passports go through a passport control at airports but I have a feeling that things are bit more relaxed now.