Highly skilled authors have always been able to compose multilinear texts, even multilinear arguments, without the assistance of computers. Plato is a good example. I don't see how today's hypertext really changes this at all, except perhaps by giving those of us with less meteoric talents access to these methods. People who think of hypertext as ushering in something like a new, democratic age in communications are probably correct, in a way. Which is precisely why you'd expect those sorts of authors to be very cautious in deploying hypertext against us.
Loose cannons can fire backwards.
Well, the same thing goes for any argument. But that's what footnotes do, as well as allusions, metaphors, name-dropping, and any number of other textual devices. The liberating effects of hypertext, I suspect, will really only accrue to those logically savvy enough to secure their own opinions in the face of all the snares set by others.