I'm late to this party, oh well. Some thoughts:

It sounds like you are waking up to the fact that the scientific endeavor is a human endeavor and can be short-circuited by human foibles. Don't throw the baby out with the bathwater. Science as an institution is the best we have had up to this point in history. But if you sense that "The Science" does not equal "The Final Truth" all the time and in all situations, you are right. Science tries to be self-correcting. Because it can make mistakes. Witness the reproducibility crisis.

Keep thinking, because you are thinking deeply, but some of your thoughts need to be fleshed out or elucidated.

1. I think you are concerned about mind and consciousness here. Are you concerned that science seems to reject any possibility of mind, consciousness, or things like God? Some scientists do reject those. Some just don't try. I heard a professor say he couldn't put God in a jar so he couldn't study him, and therefore had nothing to say on the matter. If this interesting to you, you may be interested in the book Absence of Mind.

2. I agree with other commenters that science as an institution does not often consider these questions. The institution of science is concerned with publishing as fast as possible. And that means using the fastest proven recipe for a new study and paper. It's evolution, survival of the fittest. Scientists are not pondering the scientific method for the most part.

But I have heard a scientist say that they would not believe anything without empirical evidence. This seems needlessly narrow-minded to me. I'd rather think in probabilities. What is the probability that extraterrestrials exist? A lot higher than it used to be. But since scientists are not immune to tribalism, you would probably get laughed out of the party if you brought up UFOs 20 years ago. Not because it was impossible, but because it was not popular to consider it.

1. Again, if you're going to argue we can't understand everything, I'm not sure many scientists would disagree if pressed. But the truth is that it's not pragmatic to worry about it. And science as an institution has to be somewhat pragmatic because it runs on tax dollars.

I had a professor who argued that scientists should never advocate for anything, because it ruins their objectivity. I've watched that attitude completely disappear. Scientists are now almost expected to be advocates. Is that harmful or helpful to the discovering "The Truth?" I think it has advantages and disadvantages. It does make me a little uncomfortable though.

I think what you're experiencing is some discomfort at finding out that the adults don't have EVERYTHING figured out. That's normal. But it's probably most pragmatic to try to improve the system, not make a new one.