I've stayed in several high end ryokans and have never had an issue with smoke. And I'm sensitive to it, too. Most of them have signs saying "please don't smoke in bed" (I know, bed is ironic in this case). I can tell you for a fact that in Kyoto the Hiiragiya, Kinmata, and Tawaraya did not have any smell of smoke in the room. You should be safe at any of them.

Also, I don't know how you're defining luxury, but the Seikoro Inn (and less luxurious but still luxurious ryokan) also had rooms that did not smell at all of smoke.

Have fun. Don't worry about the smoke thing in these places, in my experience!