I don't think the author did a very good job of making the case that people are thinking less due to the web. "Sometimes you need to get a second book on a subject and that gives you time to think" is not a satisfactory substitute for actually measuring how much thinking people using books versus the web to acquire knowledge do.
I also think the focus on clicking is a little bit misplaced. A similar argument would be that listening to a lecture is better than reading a book because a reader spends all her time turning pages.
I feel like this is a really interesting topic that isn't addressed very well by this article.