I have to say I haven't found things too bad yet, but then most of the books I read on the Kindle don't have much in the way of notes, and most of the books I read that are thickly be-noted I read as actual books (e.g., most Tolkien scholarship). Ironic that a format that shd be able to easily accommodate something like a note shd make cross-referencing more difficult and not less. Especially when audiobooks have by and large solved this problem -- I was particularly impressed by the deft treatment of footnotes in the audiobook of Susanna Clarke's STRANGE & NORRELL, where each notes was given its separate track on the cd, making them easy to skip for those who had a mind to press on, while most listeners could enjoy them as they came. But then JONATHAN STRANGE & MR. NORRELL might be a special case, since I ultimately concluded that the notes were better than the story there -- that is, that Clarke's world-building was superlative while the main plot was less interesting than the setting it took place in. That's rare.
I also admire Terry Pratchett's footnotes, which are a distinctive feature of his style of humor (or perhaps humour); a feature I think he derived (along with so much else) from Douglas Adams's HITCH-HIKER'S GUIDE. And of course in my own work I've always thought that, having learned grammatically how to construct compound-complex sentences, it'd be a pity not to use them. I'm also fond of parentheticals (a trait I share with Tolkien).** And I like footnotes. Sometimes my footnotes have footnotes (usually marked with a dagger). Sometimes I need to distinguish between two sets of notes, such as between Denham's notes and my notes in the DENHAM TRACT I reproduced in an appendix of H.o.H. And sometimes different notes do different things, as with the Notes to my commentary vs. the Text Notes to Tolkien's drafting in my presentation of the HOBBIT Mss.
So, as not just a reader of footnotes but also an inveterate writer of notes, I'd be sad to see the passing of the footnote -- but I trust that endnotes will still be with us, if a little harder to access. And if all else fails, we'll still have parentheticals.
**it's a feature I greatly enjoy in FARMER GILES, LotR, and esp. THE HOBBIT, and something I miss in THE SILMARILLION.