It’s pretty well documented during the Middle Ages that people thought it was the smell that made them ill and not any bacteria

And smell and bacterial levels are absolutely correlated

They are. But the solution to each might be different. And given the specific argument being contested here is whether beer was drank because it was considered safer, understanding their motives is pretty fundamental to that discussion.

The motives don't always have understanding of the root cause however. We knew that eating raw meat was unsafe even though we didn't know about salmonella.

That's exactly my point. This whole conversation is about whether beer was drank because water was unsafe. Understanding what their understanding of "unsafe" was, and what they considered the remedy, is central to this discussion.

Being smart and knowing stuff are not equivalent. The smartest person alive 300 years ago had no clue about bacteria and viruses. Or anything like horizontal gene transfer. Sure, they were not stupid. They still did not know a lot of things, which occasionally made them do stupid things. For example, it is well documented that people believed diseases were transmitted by “bad air” (i.e. pestilence, or bad smells) up until the mid-19th century (not to mention demons). They were not stupid, but there were some things they did not know.

I am not saying that we are any better; there are a lot of things we don’t know that will be taken for granted in 200 years. If there is still a human race.

> For example, it is well documented that people believed diseases were transmitted by “bad air” (i.e. pestilence, or bad smells) up

But that's not particularly stupid. Bad smells are certainly a proxy for diseases to some extent and avoiding them/removing their sources would also decrease the likelihood of getting sick.

> Bad smells are certainly a proxy for diseases to some extent

No, they are not. Because smell and germs are completely unrelated. There is a limited case where they are correlated (don’t play with organic waste or too old corpses), but even then it is not really helpful. This is why it took so long to understand how to stop cholera: you can have things in your water even if it looks pristine. The air is just a red herring.

It is not even helpful with airborne pathogens, as once they start spreading among humans all bets are off.