I think documents and hyperlinks are still relevant. Much of the content on the web is just formatted articles, which I wouldn’t mind receiving in plaintext and formatting myself (and indeed many services, such as Instapaper and Readability, have functions for the very purpose of stripping and reformatting text online). I think that web apps will remain relevant as far as the eye can see However, there is definitely a clear distinction between document and application, even if they are currently transmitted using the same protocols; distinguishing them from each other would allow numerous usage optimizations for documents (at the very least) such as the visual links of Xanadu and the sole usage of compressed plain text.
I always found it instructive that the WWW conquered the world and not Xanadu. X is a much more elegant, rich environment where hyperlinks are more meaningful and it would have been a better world in many ways - but it needs coordination between both ends of a hyperlink, whereas in the WWW, you write an A tag and you're done.
Turns out that dumb and simple beats smart and complex.
Ted Nelson is a great guy and deserves more recognition than he gets for Xanadu, which shaped a lot of thinking.