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I think structure is useful up to a certain level of complexity. As my tree hierarchy gets more and more deep and crowded with items, navigating the tree is a less appealing proposition. Not that I won't ever do it, but it begins to take up more time than it did when I had a fairly simple tree.
Logical linking helps quite a bit. I can link items or branches I know I will need to access a lot and put them in a couple of key branches near the top of the tree.
I think where the usefulness of hyperlinks comes in is actually at a level that helps tame the complexity of a huge tree. In a sense, it is a way to locate related items by simply using the content of your current item rather than locating and then linking external items. In other words, creating a hyperlink is like a shortcut for: "I know I have 'item x' in my database, and I want to relate it to my current item. So, I'm going to search for 'item x', copy the item, navigate back to my current item, and then paste the logical link." The hyperlink version of this could be as simple as: [item x]
To me, it's simply a matter of granularity rather than competing or overlapping approaches. Some users won't need or desire the finer granularity, but many will. Also, different information management tasks require different tools to be immediately available. Filing and retrieving information is well-served by hierarchy and search. Brainstorming or writing alternate interfaces into a set of data is well-served by hyperlinking.
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