A retro-fantasy realm largely populated by two-dimensional stereotypes who wander around mouthing preprogrammed banolities while chain-smoking cigarettes...seems familiar...
Mad Men - New Vegas?
In defense of Bethesda et alia, it is fair to say that an organic description of a post-apocalyptic Vegas could include tobacco (though they would have to somehow grow it - the tobacco used in conventional cigarettes doesn't keep for very long); Nevada has the third highest rate of smoking related fatalities of all US states. Further in their defense, my game only crashed a few times. Having said that...
Really doubt that's a subliminal message because there are so many NPC's that smoke.
If I was a soulless tobacco exec with a billion dollars I wasn't allowed to spend on overt advertising in certain ill-defined formats, do you think I might spend it elsewhere? Perhaps even covertly? In a fashion that may encourage tens or hundreds of thousands of young people to see cigarettes as a normal, everyday consumable rather than an extremely addictive & deadly poison? I might even get a few stooges to post some further encouragement on the game's forum. Not an impossible scenario, amirite? Who knows.
Relax man, have à smoke.....
Yeah, all those cigarettes and cannot smoke one!
Maybe you are just looking WAY too much into clutter.
As for smoking however, there was reportedly scientific study which showed that prolonged smoking makes your lungs resistant to radioactive particles. Prevent you from getting lung cancer if you inhale some. Quit handy in radioactive wasteland

Fallout cigarette packs probably carry this department of health warning text: Atention! Smoking prolongs your life

These studies do not anywhere state that smoking will prolong your life. The so-called benefits to which they refer can be reproduced much more safely where medically necessary. The findings generally amount to saying that lead carbonate makes a good sunscreen; while scientifically true, it will not prolong your life. In fact, scientifically speaking, it will likely reduce it drastically. The only finding of the 'study' to which you specifically refer is that an effective way to avoid inhaling radioactive particles is to destroy your lungs. Better rather to just throw out the bathwater, as you say; Quit - handy in radioactive wasteland
for most ppl cigaretters are not their kind of drug
While smoking rates are thankfully on the decline in Western countries, the same cannot be said for the rest of the world, where anti-tobacco legislation is thin or non-existent. Tobacco companies have had nearly 100 years since the discovery of chemical neurotransmission to develop and improve drugs that subvert our brain's natural function; compounds 100 times more potent than anything found naturally. Combined with the glamour of Hollywood & sophisticated advertising techniques, somewhat lower availability of public education and health care, and a general absence of concern, 'most ppl' don't stand much of a chance, IMO.
If you model your behavior after video games you deserve what you get.
People, of course, can spend hours using a detailed interactive simulation without taking anything on board. They can also watch television or use the internet and know exactly what is true, and what is misleading and/or in the best interests of another party. Because if they can't then they deserve what they get, right?