Edit: Next time I'll do a cursory googling before commenting. This is apparently an existing hypothesis for common types of bacteria such as e coli, salmonella, etc in the drink itself, not in the body.
In an age where other beverages are as easily accessible for people living in the modern world, it’s utility isn’t there any more and you are left with all the downsides.
Coffee, tea, and tobacco, became at least as widespread once global trade made that possible. Coca was late to the party because it doesn't grow well outside of its native region.
Cannabis is an odd one, in that it was extremely widespread and making solid inroads in Europe and North America, when it became a weapon for United States racial policy, and a jobs program for federal police after the repeal of Prohibition. Coca and cocaine got caught up in the same dragnet.
Opium and its derivatives are genuinely pernicious and attempts to normalize their use outside of medicine have been resisted repeatedly throughout history.
Which leaves psychedelics, which are... weird, and also were largely unknown until some anthropologists in the 40s and 50s drew attention to them.
The history of 'modern' drug prohibition owes more to politics than the inherent properties of the substances in question.
You can definitely see the benefit for an ancient civilization, since you're able to store many more calories which allows you to grow a much larger population base. But like many things associated with the move to agrarian civilizations, being good for the civilization doesn't necessarilly correlate with being good for the individual.
You get alcohol when fruit spoils. Our experience with it is quite literally as old as foraging. This doesn't tell us anything about how harmful or not harmful alcohol is.
As far as ubiquity, plant-based substances had to follow migration or trade routes to gain use outside of their native habitats. Alcohol was coextensive with any food .
The addiction rate for cocaine/heroin/meth may be higher, but the negative effects of those drugs mostly stem from the high cost (theft) and insane profit margins (murder). If a heroin addict could get their supply for $5/day (and have it be pure heroin w no fentanyl) then nearly all of the negatives would disappear.
Meth has lot less sympathetic side effects than dextroamphetamine per unit of dopaminergic stimulation, this simple difference enables abuser to consume ridiculously large dose and those high doses are destructive.
https://astralcodexten.substack.com/p/know-your-amphetamines
[41] https://www.ncbi.nlm.nih.gov/pubmed/23688691/
[43] https://www.ncbi.nlm.nih.gov/pubmed/3355623/
[45] https://www.ncbi.nlm.nih.gov/pubmed/7299411/
From my experience with Vyvanse I find that amphetamines have a dose response function with linear and exponential steps. 15mg is barely perceptible, 30mg is like a coffee without the anxiety but it last 8 hours. 45mg is like 30mg but a little longer. 60mg in 2 doses (first pill at 7am and next one at 9am) is a perfect treatment against my ADD. Once I tried 90mg and it was terrible, I experienced bruxism, anxiety and hyperacidity for 18 hours. I am sure that I would develop the problems you listed if I were to take 90mg a day but 90mg of Vyvanse is supratherapeutic...
1: Link 41 is about abuse (supratherapeutic and frequent doses). Link 43 I can't comment as I don't have acces but it's an old paper from 1988... Link 45 is about abuse again. Link 46 is about accidental ingestion by a baby. (a therapeutic dose for a teenager is clearly supratherapeutic in a 8months infant) Link 47 is probably about abuse (the abstract talk of reversible consequences of dose escalation) but I don't have acces to the paper.