I guess it's not surprising that there should be few native hypertexts in the scholarly discourse community when electronic scholarship in general is still meeting pockets of resistance.
Much of this resistance comes not from scholars themselves but, not surprisingly, from the administrative apparatus of the scholarly community. Many scholars are not recognized, or are given less recognition, for electronically published material.
(Christina Haas once told me a personal horror story about her own department which maintains a list of forty-odd journals in which it is considered respectable to publish. Naturally none of these is rhetorical, and none is electronic.)
This resistance originates partly in the general "papyrocentric" attitude of the University bureaucracy (to borrow one of Stevan Harnad's best terms). But it is facile to lay all the blame at the door of bureaucracy. It probably also has a lot to do with the fact that the electronic medium has not yet evolved very clear and reliable standards for tagging electronic publications as to quality. It is not easy to tell a high-class peer-reviewed journal from a discussion list.
Another site of resistance is the scholarly publishing industry, which is in the habit of offering electronic versions of paper publications at an extra charge. They just don't seem to get it.
I say a lot more about all this in my article, "Kick-Starting Electronic Scholarship: Stevan Harnad's "Subversive Proposal," and Stevan Harnad says even more.