I have done this layover many, many times over the last 5-6 years, arrive HND at 4-5PM and depart the next day at 10-11AM and my bags were always checked through to final destination, never had any issue with it, it was a given, but check-in would always ask if I wanted it checked through or if I wanted to retrieve my bag and check-it in for the connection the next day. I would then just have by small cabin wheelie and laptop bag with me with overnight gear in it and go to a hotel. The initial JAL agent gave you the wrong information.