How to handle a common misconception when writing a Master's thesis?

I agree that option 2. is not good. If you want to mention the misconception but avoid shaming anybody, you can write something like

"While the belief in the 1980s and 1990 was … it was proven in […] that in fact…"

That way, no one is blamed. If, however, you feel that you need to explicitly mention that still some people follow the old belief, you should back this up by citations and I don't see a way around option 3.

If at all, I would add the reference to the now anachronistic misconception in a footnote. In my opinion, you should not introduce any obsolete information in the main body of your thesis as long as the actual misconception is not a scope of your work. Plainly use the correct data with source information. You do not need to keep old misconceptions alive.

However, if you think you need to mention the misconception, I would add a footnote where you discuss the material properties. In the footnote, you can discuss the evolution of the material data in any level detail you think appropriate and back this even up with references to the now faulty sources. Thus, your thesis remains focused on your actual work but still does include the additional information for the suspicious reader.