I don't think there would be issues.
Thanks for the swift response. Since Canada doesn't require a visa for Japanese citizens, I'd expect that she'd be able to come and go but when it comes to officialdom I don't want to leave anything to luck/chance. For instance when I was dealing with customs to bring our personal possessions into the country, the agent refused as proof that I'd been living in Japan for the past twelve months:
+ my japanese driver's license
+ a notarized translation of that document
+ the spousal visas in my passport dating back to 2007
+ the family registration document showing the dates of our marriage, the 2008 birth of our son, etc
I'm left with the impression that the whole thing is left to the decision of the agent in question, which makes me doubtful.