Isn't that what they've been doing? San Andreas has drugs, prostitutes, and more vulgar language than ever before. Sure they might have taken out that pill in SA, but did you do play the mission where you burn the weed and then have to drive Truth's van impaired from the drugs? That's a much more explicit representation of drugs than the pill imo. It would be nice if you could provide some more examples for your argument so I could see where you're coming from.
Also, I don't think that stuff contributes all that much to atmosphere either. Rather it's the level design, characters, and setting that shape the game's atmosphere (at least for me).