I agree that the inherent qualities of e-reading will provide new solutions to old problems.. It's not as if printed books were perfect in their solutions, after all: If you obtained the same book by a different publisher, using page counts for references could be rendered useless.
In most cases, chapter, section, length/position in text and indexing information will suffice to make most books easy to access. The page metaphor will eventually be considered a quaint way of expression, like the "act" of a play, the "movie reel" and the "commercial break"... still used, but not the predominant form of media metaphor, replaced by electronic file and display-based metaphors.
Hmm... will we replace the "chapter" with another phrase?