I agree that we should question everything, and use critical thinking to try and find the truth about these kinds of issues.
But that doesn't mean we should simply accept and believe hypotheses just because there's a possibility they might be true. That's the opposite of scientific critical thinking, especially when there is overwhelming evidence that is contrary to the hypothesis.
Yes, of course it's possible that vaccines are a covert plan to sterilize and depopulate the human race, weaken their immune systems so they rely on drugs made by Big Pharma, or change their brain chemistry to make them more susceptible to government mind control.
But until we get some good evidence that any of this is true, it makes no sense to believe it. Especially when the evidence that vaccines have saved millions of people's lives and are relatively safe is overwhelming.
Extraordinary claims demand extraordinary evidence.
To 'believe a hypothesis' is a nonsense phrase. At least as I define things. By my definition a hypothesis cannot be believed. It sits among other complementary or mutually exclusive hypotheses to be analysed against incoming information or new formulations of information. Of course it can easily be rejected for a variety of reasons, but NOT simply because it is out of fashion in some way.
It is also the case that one can expect 'good evidence' to surface only when there is a mechanism by which that can occur. If there are mechanisms by which evidence is limited in quality then it makes no sense to reject a hypothesis by virtue of lack of evidence. In my analysis of the vaccination issue I see many many efforts to support one hypothesis and discount a competing one in very dishonest ways.
There are strong hypotheses and weak ones. A good example of a weak one is what I tossed out about metallic components in brain tissue being deliberately installed to make some possible electromagnetic impacts more functional. I classify it as 'my own' because as far as I remember I came up with it on my own and in a response to the question of why there might be a desire by some to get aluminum (and a bit of Hg) containing vaccines injected into a baby on the first day of life. Even more, why do so when it seems that the vaccine itself has at best an ambiguous benefit.
My chief argument against the hypothesis that electromagnetic means are sometimes used to manipulate human development and behavior is that such programs could be leaked by insiders and/or detected by outsiders. With the advent of sensitive and flexible analytical tools available to the masses, it's hard to imagine that someone somewhere would not be interested enough to study and detect such programs. I've not seen it, but then I've not looked that hard either.
Going back to your suggestion that MKULTRA did exist 'but none of that shit really worked' I would say that this is simply unknown. If the official story is to be believed, most of the records were destroyed. It is an interesting subject generally for a variety of reasons, and it did seem to be a fairly long running and well funded program which in and of itself calls into question the assertion that none of it worked. Where I go from here is to pay attention to some continuing similar research (e.g., being able to pull a graphical image of a face out of a person's thought patterns), and analyze the lives of some of the people who were known to have participated in some of the MKULTRA experiments such as Ken Kesey and Ted Kaczynski (aka, the unibomber.)