What's wrong with the traditional folder full of symlinks? This article doesn't talk about symbolic links at all, and they would solve all the "problems" discussed here.
The only problem symlinks can address would that of having files available under multiple locations. But that's still strictly hierarchical and bound to become a maintenance nightmare soon (just think about file renames).
Tag based filesystems are indeed an interesting idea and a somewhat logical next step from the traditional hierarchical fs + desktop search tandem that is commonplace now.
I do believe that desktops will lose their significance over time and the web experience will be the next thing.
And then it may even migrate to the OS itself, because it will be the familiar thing.
This would end up being a maintenance nightmare for different reason, though. You'd end up with two dirs, for example work/projectX and projectX/work, with some files in one and some files in another. Strict hierarchies don't map to tags.