The worst thing ever is end-book-notes (or end-chapter ones) in a paper book. I have the habit of "precise reading", e.g. I usually read books from first to last page without skipping information. The "end-notes rich" books are the worst reading experience for me (bottom page foot-notes are OK).

When I write text I quite often use footnotes - they are special for the organisation of the text, adding kind of additional dimensions to the main narration.

I don't (or very rarely) use ebooks, so hard to tell.