JJLL mentions an interesting point about not defacing holy books. However, when I was in yeshiva high school, not only did I take extensive notes, but I wrote many of them in the Talmud margins (Believe it or not, Rash"i and Tosfot as well as all the others aren't the only ones vying for margin space!) Admittedly, a large reason for the note taking is that eventually I would be tested on these things. However, in many yeshivot, and kollel, etc, today, I still see people writing notes, usually in a note book. (Now, with technology, some are using their laptops or tablets.)
But, perhaps, one reason many are NOT taking notes may be due to the nature of learning certain subjects, esp. Talmud, itself. For many, the task of the learning itself is its own reward, not necessarily memorizing all the facts, commentary, and nuances. Even in my yeshiva, many sections of Talmud were reviewed sometimes multiple times. Part of it was to memorize, thus, in a sense, precluding the need for written notes. Another motive was as I mentioned - your focus is on the learning method, itself and moreso the discussion of these concepts with your chevruta (learning partner.) The idea is for each to come up with his own analysis and discussion of the topic, asking each other questions, coming up with your own answers, and having a "debate" - much in the same way that the Talmud itself does. Perhaps, if each person took notes, this would greatly disturb the flow and mitigate the spontaneity of the discussion between each other.