I’m pretty much in agreement with you here, and think part of the problem was the overselling of the concept of “hypertext” per se and the underselling of the more general notions of multimedia/new media authorship; in addition, the idea of a total free-play narrative that seemed suggested in some the early hypertext theory never seemed to me to be easily melded with the other desiderata of narrative (and to a lesser extent poetry).
Since you asked “Where was our poststructural theory then?” of the moment when the web became commercialized, I’ll just point at my 1996 Postmodern Culture essay “Hypercapital,” which offers an explicitly poststructuralist critique of certain hypertextual dreams. Once a skeptic, always a skeptic, I suppose; although my target in that essay is more about the promises for cultural transformation via hypertext replacing “standard” text, than about hypertext literature. I was pretty young then and there is stuff I would change about it today, but there you go.
That essay loosely served a few years later as the basis for one of the more experimental pieces Postmodern Culture ever printed:
Daev. Gl=umläia,”Hiiperlexicoasemeopara[=tastrophism: Geo-graphist-insenstiorsme.” Postmodern Culture 12:1 (September 2001)
which is of course partly broken now, but that was kind of the point.
Please forgive the self-promotion, but it seemed to speak to the topic awfully directly, and what is the commercial web for anyway, etc.