Absolutely. Individual scientists are frequently wrong, misinformed, make mistakes and so on.

thx for your trouble. What is your occupation?

Unemployed. Graduated this year with a physics degree.

Sorry, but this is my area, and no one I know states the Riemann Hypothesis as fact.  Mathematicians by training have pretty rigorous standards for what they are willing to call a fact.  However, being creatures of abstraction not bound to the real world, we are still happy to write speculative papers built on the premise of RH, which are clearly labeled as being conditional and not factual results.

A slightly better example from math would be the Axiom of Choice.  Again, you won't find a mathematician who claims it as fact, but entire areas of mathematics would be unusable without this assumption (the effect is large enough that you wouldn't routinely call out the use of AC unless you were addressing a wider audience).  Even still, operating in this way is pretty credibly justified by Gödel's and Cohen's consistency results (we essentially know that AC will never be proven or disproven in the future, not without taking down some more fundamental axioms).

Generally speaking, much of theory will have some basis in what we already know to be true, or at least scientifically tested/vetted as true. I will grant you that there are some theoretical physicists out there who've proposed what we would think as rather crazy ideas, however, you have to understand that quantum mechanics allow for some extremely peculiar and to be honest, alien outcomes. We just don't see the world on a quantum level, and it's difficult for us to imagine how things can work the way they do there. For example, getting something from nothing (See: Lawrence Krauss, on youtube) as an explanation of how the big bang is a completely reasonable event in quantum mechanics.

To answer your question though, no, I don't think people go to far in scientific theory. If the theories were accepted blindly, without proper vetting I'd have a problem with it. But, part of being a great scientist is helping to prove others wrong/right, through extensive testing and research.  I will say what many people say is either assumed or made up, is simply a lack of understanding in the field.

Even if science is too focused on assumptions, it is those assumptions which helps us advance. In mathematics, Perturbation and Chaos theory are possibly the best examples of how assumptions can help us understand aspects in the real world which we would have otherwise not understood such as chaotic behaviour and how boundary layers work.

Saying science is too much about assumptions shows a lack of understanding of science to begin with.

There will always be assumptions about everything. You keep asking the "why" question and you'll always get to the point where an assumption will be made about something.

I think you're confusing it with religion.

Oh, yeah, I'm not saying the papers state is as fact. I just mean a lot of work has been built on assuming it is true that would disappear if it's proven false.

Is it possible to quantify (even informally) how likely RH is to be false? Or AC?

The King of of all sciences physics is based on few assumptions.
Chemistry the next man up is based on more assumptions.
The rest are based of more.
The original poster seems to know very little about science.