I like the concept of indices but a lot of indices i see (like in textbooks) are incomplete. I have to think "ok what might be related to this?" And it certainly is not an easy problem!
Bookmarks are folder structure. Theoretically you can bookmark the same thing under a different part of the structure of course. I've never really seen people do that though, except accidentally because they found something the liked, bookmarked it in on place, later found it again, didn't remember they already bookmarked it and bookmarked it in a different part of their folder structure. In a way they also "tagged" except that the actual bookmark, the thing is not the same. It's a copy. If your bookmark goes to some address that might change while pointing to the same actual thing, you'd now have to update (and first find) a multitude of bookmarks in your folder structure. A file system that has hardlinks could implement "tagging" too :)
The tech was cool, but I think they ran into the issue you just suggested - people dont really bookmark, and it was hard to make people see it as anything other than a bookmarking tool with categorization.