Nuttall notes that "speed, enjoyment and comprehension are closely linked with one another" (1996: 128). She describes "The vicious circle of the weak reader: Reads slowly; Doesn't enjoy reading; Doesn't read much; Doesn't understand; Reads slowly. . ." (p. 127) and so on. Extensive reading can help readers "enter instead the cycle of growth. . . . The virtuous circle of the good reader: Reads faster; Reads more; Understands better; Enjoys reading; Reads faster. . ."
Thus, I would conclude that any activity, be it note taking or a similar endeavor, if proves to be disturbing the reading fluency of the agent, it could result in unintended secondary consequences, as such to foster an aversion to reading, supported by the deduction in reading pleasure and comprehension.
At the end, the agent could find itself spending less time reading, the main culprit being the very methods which it sought to maximize reading productivity, as such methods proved to be destructive for its reading fluency.