I can see them fit at Mass Effect.
They are in the future,and until then scientists found ways to make people smoke without harmfull effects.
You can read that at the latest book of the franchise,the one the Illusive Man is the protagonist.
Really? I've never heard it mentioned or wirrten anywhere that smoking is not harmfull in the Mass Effect universe, I have ready every little bit of information out there on that particular franchise, or close to it.
People in Mass Effect smoke because people smoke in real life, you have to admit, as harmfull as it may be, The Illusive Man just wouldn't have as much charm if he wasn't constantly seen with a drink and cigarette in his hand.
EDIT: Also, every character I've ever played in a game that allows it has been a smoker, granted that's not many, but still. I have done my share of virtual smoking, I have never smoked a cigarette in my life, I smoke a cigar maybe once or twice a year but that's hardly the same. So no, smoking in games does not make you smoke in real life, anyone who honestly believes that is in need of some education.