The Little I Know – The Baal Shem haKadosh was said to be able to send his neshama to the olam ha’atzilut and back at will. I highly doubt he wouldn’t have been aware of any negative effects of smoking simply because the scientists of the time were ignorant of it. It could very well be that because he was truly smoking l’shem shamayim and not just for his physical pleasure, it wasn’t mazik him. There was a story of Rebbe Nachman that he used to smoke his pipe with certain kavanot in order to achieve the spiritual aspects of the ketoret in lieu of having an actual Beit HaMikdash so I would have to assume his great grandfather the Besht was doing so as well.
In more recent times there were tzaddikim like Rav Kaduri who was a very heavy smoker but lived past 100. He once asked one of his students to pick him up a pack of his brand of cigarettes (I forget which ones he particularly smoked) but the student brought back another brand claiming the one he requested had run out at the store. Rav Kaduri refused to smoke them and told him something to the effect of, “It doesn’t make a difference for you which brand it is because when you smoke you’re simply having a cigarette. It makes a difference for me because when I’m smoking I’m doing something much higher.” That wasn’t his quote word for word but that’s the gist of the story. So obviously he had secret spiritual intentions when he smoked and I’m not sure, but it could be possible that his long life shows that the physical effects of smoking didn’t hurt his body because of that. Just a thought. Additionally – the tobacco the Baal Shem Tov was smoking (I’m pretty sure I’ve heard it b’ferush that it was tobacco and not weed or anything else) was probably a lot less dangerous for your health than is the tobacco in modern day cigarettes as these days they add in a tons of nasty extra chemicals (including an ingredient from rat poison!)