In an exhaust pipe for a smoker I seriously doubt it will matter if the metal is galvanized.
At very high heat the galvanized coating can off gas and the fumes can cause what is caused "metal fume fever", which is the body's reaction to inhaling the fumes. This is common with welders in enclosed areas with certain metals. The key is the high heat that causes the metal compounds to fume or off gas. Unless you are welding, brazing or soldering galvanized metal, I doubt you will need to worry.
In smoking you "might" see those high temps in the fire basket, but I doubt it is even possible to get the temps high enough in a smoke stack to matter with a galvanized stack. So unless you have galvanized metal in your fire basket, it should not be a problem. Also once you burn off the coating it should not be a problem either, even if your fire basket is galvanized. So once a smoker has been burned in and seasoned I don't think it would be an issue again.