I don't think they're trying to solve this issue directly. This is intended to be used as PKM (personal knowledge management) system.
You are correct in any case that this is a hard problem and I would love to get some perspective from the author on implementing such a system org-wide.
Not sure I agree with your PKM point. It feels like it fits well for company/project structure. Reading his forum and a bit into the article it seems to advocate a "librarian" that keeps the system correctly categorized. I think he mentioned somewhere that this system doesn't fully fit PKM. I remeber some example of categorizing photos according after vacations, but running out of numbers. But I must admit I don't fully remeber the arguments.
You are correct in any case that this is a hard problem and I would love to get some perspective from the author on implementing such a system org-wide.