I cannot remember when I saw a rental agency that allowed smoking per policy in their cars, however that doesn't mean people follow the rules.
I personally only have had issues with Enterprise when it comes to cars that smelled like smoke, but all agencies have vehicles in their fleet that have been smoked in.
As for Dollar/Thrifty, I think your chances are as good as any other to run into a smoking car. As for the vehicles themselves, from my personal experience I find that most of their cars are not kept as clean/maintained as cars from Hertz. Hertz is my preferred rental agency, but I have ventured out in the past and in those times I have found being underwhelmed.
Never had a problem with Dollar. The last car we had, was brand new with 7 miles on it. But they've all been very clean, never smelled smoke. I'm sure people do break the rules and smoke, but if I smelled it, I would just exchange the car.