Is it okay to use the same footnote with exact same words in two different chapters of a thesis?
Your question is predicated on the largely false assumption that there are detailed, sentence-level rules about what is and is not accepted in "academic writing".  There are no such rules.  Writing is a creative activity.  Use whatever words, footnotes, and anything else most clearly express your ideas.

If you are writing a thesis, check your institution's rules for theses. But I doubt they will include anything this specific.