When I read this chapter of The Shallows, I was completely baffled. The way in which he described people reading articles on the internet and clicking links as they come is completely foreign and unrealistic to me. I guess it must happen, based on the research he cited, but I don't know anyone who reads that way. Personally, if I'm reading an article with links to other articles, I may open them in a background tab to read after I have completed the initial article. Also, with services like Instapaper, Readability, Pocket, iCloud Reading List, and, of course, Diigo, the issue of being distracted by ancillary material on a website that is being read can be mitigated. The examples he cited in this chapter seemed like worst case scenarios of inexperienced web users, and I saw them as essentially straw men.
Also, I think Martin made a great point with regard to the use of ebooks specifically for reference material. I love being able to use the Logos application to view multiple translations and additional commentaries for bible study. I think it is fitting that you also had the interview regarding HymnSoft and the new hymnal on this episode. I, for one, cannot wait to have a digital hymnal to use on my iPad at church. It can't come soon enough for me.