Installing smoke machines along the expressways might not have been such a good idea, no matter how cool it looked ...
More seriously, this has been something that has always made less than a lot of sense in ShadowRun. Even back in first edition a lot of power was coming from nuclear plants (no air pollution), and there were various other factors that I always thought made the high air pollution seem doubtful. Basically the desire for cool science fiction future stuff was in a bit of a battle with the dystopia stuff, and they just kind of waved their hands and said "you get both!"
I guess the argument is that with ineffective government regulation, industry has ripped out all the pollution controls to reduce costs. Places are burning coal if they need heat in their processes, and maybe some power plants are running on coal too (and coal is a huge, huge, factor in smog and acid rain -- or at least lower grades of coal in plants without pollution controls are). Or heavy petroleum products (don't burn very cleanly) which are heavy with sulphur (don't have the same requirements around sulphur content that we have currently).
Plus, in the barrens people aren't on the grid in many cases, so are burning whatever they can get their hands on for heat and cooking. Ships and planes are burning whatever is cheapest, blasting out large amounts of pollution. Agriculture is using fertilizers and pesticides with little regard for their health effects, and those blow into cities. In Seattle you get sulphur dioxide coming from the local volcano (if you've had the change to visit the the volcano on the big island in Hawaii you'll realize how caustic even low levels of this can be).
Personally, I don't make a big deal of it in my home game.