I missed this article when it was first published. I hope you can still access it when the New York Times puts up its pay wall.
In any case, there seem to be two extremes in readers. Those who never mark their books, never adding marginal annotations, and those who mark up their books heavily, underlining and annotating. For many of the later type, annotations replace notebooks. I belong to neither, I mark up the text, taking note of passages that I will later transcribe, but comments are reserved for my (now electronic) notebook.
These two styles seem to survive into the electronic world. Some people need to mark up their PDFs, for instance. Others transfer the notes into note-taking programs. (So, I am not entirely sure, the premise of the article is correct.