Having just finished Cormac McCarthy's "Blood Meridian" -- a book which in two typical pages produces the words: "squailed," "vadose," "bated" (not in it's normal sense), "terra damnata," "carreta," "monocline," "sleared," "rebozos," "fusil," and "clackdish" -- I have an opinion on this post from O'Reilly on eBook Annotations
The only thing worse than having no annotations in a difficult text is having annotations: I hated those overly-footnoted texts of Shakespeare and the classics that combined actually interesting footnotes with constant vocabulary (the meaning of "terra damnata" is obvious and if "fusil" reminds you of "fusilier"...).
On the other hand, I wouldn't at all mind some kind of annotation and analysis to accompany a challenging work like this. eBooks actually have the opportunity to have the finest user experience possible: allowing a spectrum of annotations (from vocabulary to book-summing essays) to be shown, or not, wholly under the user's control.
If you just show all the links at all times, then the reader never knows the difference between "Footnote 538: A type of flower" and "Footnote 539: This is considered the central passage of the text..."