If you think scientists don't know that correlation does not imply causation, I'm happy to report to you that they, in fact, do. Separating out incidental correlation from causation is actually kind of the point of science, and by extension, medicine. The primary population that gets it wrong is the people that read a single study, and immediately conclude something based on that one study, like "oh hey ketogenic diets reduces bad cholesterol, it must be super good."
And it's simply intellectually dishonest (at best) to state that the motivation of the researcher is only to increase their paper count with presumable producing junk science, without presenting a shred of evidence to support such a claim(talk about bad science).
You said that all cause mortality increases on a ketogenic diet, and this study shows no such thing.
Because that means that you're grabbing a large cohort of people, fixing their diets, and following them until a good number of them die.
The timescales required here, not to mention the cost, means that such studies are virtually unfeasible.
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> The risks of all-cause and cause-specific death over an average 6.4-year follow-up rose with each fall in carbohydrate intake (see table), and remained significant after adjusting for all available factors that might have influenced the association (Model 2 in the table).
Quoted from the study.
It suggests exactly that thing. I suggest you read the study again.