A friend of mine has dual citizen ship.both amarican and canadian.
He visited Japan frequent on his Amarican pasport (not eligeble for working holliday)
and he did so also after leaving a pic and fingerprint on at the airport customs as we al have to do nowadays.
Hey aplied for a working holliday visa on his canadian pasport and had no problem getting one , also no problems at customs.
THE ONLY PROBLEM HE HAD
was when he applied for the workin holliday visa.
He had to go to canada for an interview at the Japanese embasy ..