When we lived in Japan in the mid '90s, we rode our tandem in many places, putting on about 5000KM in that time. We rode mostly in Shizuoka ken, but also in many of the adjoining areas. Also did a three week tour in 2004, of which all but three days was not in Nagano prefecture.
Our only interactions with the police were when we were invited in for tea:)
From what we were told, it has been a non enforced law to be used only if there is an accident. The purpose was to prevent kids from riding multiple people on a bike, tandems were not envisioned by the authors.
you can read about our 15 year old exploits at:
http://www.gtgtandems.com/japan.html