Should I comment on a cited paper in the paper-review part of my master's thesis?
I'm not entirely sure about what kind of publications you are talking about when you say 'published by vendors' (white papers, brochures, user manuals?). But if you are referring to scientific literature, my answer is: by all means. 

I don't se why you would refrain yourself from commenting the possible limitations or drawbacks of published methods. Just stay modest and consider the possibility that these publications came out a while ago and that the general knowledge in the field improved since then. 

Being critical, if done properly (give objective reasons), is certainly something to be encouraged at the Master's level, and yes the appropriate section for this is the "State of the art" section.