Should licensed code be acknowledged in Thesis
Generally in a thesis or in an academic paper in my field (numerical modeling, engineering) people try to mention which languages and library they have used to implement an algorithm or a method. If you use a commonly known algorithm which was implemented in a library (whatever the license of that library is) I think it would be most appropriate to mention which implementation of the library is used in your methodology section.

The are numerous reasons for this. First it gives credit to the people who wrote the library. You will often see on library website a paper to cite which is the "defining paper" of the library. It is good to acknowledge that. Second, if there were to be a bug found in the future in the library or some limitation, this could then be easily traced back to your results to justify surprising results. Thus it is more rigorous to state which implementation and which version you are using.

In all cases, I believe that crucial libraries that implement complex algorithmic elements should be acknowledged in the methodology section, along with the library version and a reference to it if such a reference exist.