What is the significance of the Master thesis (topic and quality) when you apply for a job in the industry/academia?
Does the topic that you work on as a master thesis affect your future job if you apply to a position that is not that much related?


By applying to a position you are not that familiar with, you will compete against people who know more about the job than you do, starting with a disadvantage. However, as AJed said, companies are sometimes looking for potential rather than technical skills and showing other skills during a job interview can prove really useful.


  What about the academia?


To answer this question, I will assume that you mean "looking for a PhD position". I think it will be even more difficult to find a PhD position if you change field (please correct me if I am wrong). Indeed the ultimate goal of a PhD program is to make the student an expert in his domain and the commitee might prefer choosing someone with little experience than no experience at all in the topic.

Finally, there are plenty of applied research fields related to Human-Computer Interactions so before you switch topic I advise you to check some of them in-depth.