We need to have a way to figure out what to tell people to do, and we're doing that, whether you like it or not, with imperfect information.
Also not for nothing, this data is not "more or less garbage". This is about as good as we can do in science right now, and honestly your tone is pretty terrible. It sounds like you want religious levels of certainty and you feel you deserve that.
Science doesn't get much more certain than this (and this is far from very certain in any sense), there is no "better" way to do things that the researchers just lazily didn't follow here, and your suggesting that such is the case is ignorant and selfish. You should feel bad for what you've written here.
A well designed RCT isn’t much more certain than this?
Observational studies are hardly the peak for scientific knowledge.
The standard shouldn’t be “we did the best we can” for the sake of publishing. It should be “is what we’re doing useful”.
> I’m guessing this study will make some institutions think/rethink their guidance on coffee consumption.
This is the major issue with all these kinds of studies. The absolute last thing they should be doing is influencing public policy. Data that’s more or less garbage but you treat it like it’s solid because it’s “science” is harmful.