Count me as another who finds endnotes really annoying. I also dislike the conflation of references with actual “footnotes” that provide additional information.
I read semi- to seriously scholarly books in an assortment of disciplines (biology, most social sciences, history, and religion - plus anything that catches my attention, which can light on some odd things at times). I use the “two bookmarks” method to keep track. Another practice of mine is to glance at upcoming endnotes to see the number of the next one that contains comments. I then go back to reading, ignoring the intervening endnotes (if I don’t get so buried in the text that I can’t remember what’s the next endnote to read; that happens sometimes, and is thoroughly annoying).
Endnotes have existed side by side with footnotes for a long time. That doesn’t mean that serious readers must therefore like them, or accept them as inevitable. However, if ya gotta give me endnotes, give me a separate bib, so I don’t hafta go back and pick out the references I want the hard way.
Given modern software, footnotes shouldn’t be that hard to manage in the right package. I therefore feel this is not a reasonable excuse. It’s merely a matter of getting the right software. I believe that all three forms of readers’ helps (notes, bibliography, and index) should be in every serious (not just scholarly) book (they’re not), and that they definitely constitute “added value” in any serious non-fiction book.