The best way to find out when the establishment is hiding something or when a "conspiracy theory" is true, is to carefully read the "fact check" that is pushed everywhere.

If you know what to look for you'll spot them quickly. How many times they add an unimportant or needlessly specific detail to a claim and then only refute that detail. Or that throughout the entire thing it's a series of mild caveats with no hard data, or obvious hand waving like "both sides were there" without addressing the difference between them or going out of their way not to mention the massive discrepancy.

A simple example from the other day: 

The Claim = "There are zero cases of autism or chronic illnesses in Amish community because they are unvaccinated"

The Fact Check = "Some Amish get vaccinated too. There are definitely cases of Amish having cancer, chronic illnesses, and autism."

What they DID do:
• Used "zero cases" as their very easy metric to shut down because its an impossible claim, rather than addressing the obvious point of the claim, that there's a vast difference.
• Pointed to some specific person saying this thing and the loose information they had to back it up at that specific time. "He based this off interviewing a few dozen Amish, NoT SciEnCe." Rather than again, actually talking about the issue or looking at real data.

What they did NOT do:
• They never discussed the vast difference between the two populations. 
• They never shared investigations or brought up information about whether there was actually a difference between the vaccinated or unvaccinated Amish, even disregarding the difference from the wider population.
• They shared the same old post-hoc uncontrolled studies of vaccinated populations, without any data from the Amish or a less vaccinated population to compare to, in order to justify the same old "it's safe" narrative.

Basically it was a lesson in political framing and narrative posturing. The fact is, either they directly refused to bring up the hard data and actually address the issue, OR they couldn't find any real data to support their "fact check" (ie. they had zero facts to actually refute the problem posed) revealing the legitimacy of the concern, rather than it being a falsehood.

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It's important for us to understand that everything you read from everyone has a degree of unreliability. The "conspiracy theorists" are incentivized to believe and find info that proves that every disease since the beginning of time was caused by Big Pharma. While the establishment is going to twist and caveat everything into confusing nonsense and simply try to make anyone who says anything that deviates from The Narrative™️ seem crazy, strawman their claim, or associate them with someone with no credibility. This is universal.

It's often in the defense that you will find the threads you should pull on. It's what they DONT refute. What they refuse to provide data on. Or the issue they avoid talking about that will reveal where they have no foundation to stand on.

For the people who know what to look for, you'll find the "fact checkers" themselves to be one of your best resources for finding out whether or not they are completely full of shit.