First off, I'd like to say thanks for using MKD as a reference. Also, I'm amused because that's probably the mildest thing in that fic. XD
Second (which probably has to do with the above), I never really saw smoking or drinking as something really serious. Maybe it's just that I grew up thinking that stuff like The Simpsons and Married With Children were perfectly normal for family viewing (because I'm a 90's child), but if I see something like smoking or drinking in someone else's written work, if the fic isn't centered around cigarettes or alcohol (and not in the "very special Blossom" way) and is more of a passing, "oh, hey, by the way, there's cigarettes and alcohol in this world," then I really don't think twice about it and am more likely to go, "Oh, hey, there's cigarettes and alcohol in this world. What's that Mudkip doing?"
In other words, I never really felt the need to censor things like that, really, because I never really thought of it as all that severe, particularly if the character isn't getting drunk or abusing something a bit more extreme than a cigarette and if the fanfiction isn't getting fixated in a sense on it. Which is really just another way of saying there's just worse things you could possibly do in a fanfiction that would really need a warning. You could add one if you feel the need to be safe, although I personally wouldn't bother unless I was doing a bunch of other stuff on top of a brief mentioning of alcohol or a cigarette in someone's hand.
But that's probably just me. I mean, I also grew up in the "very special Blossom" era, so I guess I just sort of expect people to understand that just because a fictional character is puffing on a cigarette every now and then doesn't mean they have to. XD