Trust me, the quickest way to know what David Abulafia has to say about Emperor Otto's dealings with the Hohenstaufen is to scan. If all I wanted was the Battle of Bouvines, then sure, a search in an ebook probably does the job. But scanning an ebook is incredibly frustrating because it's so sloooow. Add to that my spatial memory--I can remember that a wanted passage was on the verso page about mid-way down--and the physical book still has it all over the ebook.
Gosh yes, THIS. Thing is, I also do this for fiction. Author drops a new hint on page 257, which makes me go, "Oh HEY, what if this guy is THAT guy's brother??" If I'm reading a physical book, I flip back and find the previous material that I think connects up on this (which is easy to do because I remember that spatial element, and where it came related to other happenings in the book, it's so quick and easy) and see if it says what I thought it did. I can't do that with an e-book.
Not to mention the unbelievable pain in my arse that footnotes represent on e-reader. All notes are endnotes to an e-reader (or at least to my e-reader), and that quick flick of the eyes that doesn't interrupt the reading becomes an arduous process. It's possibly that part of why I stopped reading Jay Kristoff's
Nevernight was because I couldn't be bothered with clicking through on multiple footnotes per page, and a lot of the good jokes were in the footnotes.