I just want to share my 2 cents as I recently booked 1 night at a ryokan in a hotspring (onsen).

Make sure you select the room and services that you want! There are several choices: Twin Room, Japanese room with Western-style beds, Traditional Japanese rooms, no meals included, breakfast included, breakfast and dinner included (half-board) etc. The options can be confusing and overwhelming! I found JapanIcan gives the best prices for ryokan.

I believe many of the rooms accommodate smokers although some don't so make sure you look into that if you (or your kids) are allergic to smoke.

Happy travels!