Symlinks can work, and I've used them.
My advice to people is usually, though, that your brain will sort it out for you. And it really does.
The canonical example is "home insurance". Say you have a category of "home" and a category elsewhere of "insurance". Perfectly possible.
Which one does it go in? Well, you designed this system. Your brain came up with it. I've found that in nearly all cases, you just know.
I see where this may fall down in a shared environment (work), which is why I advocate (in one of the many unwritten posts on my as-yet-to-exist blog) for the role of a 'librarian' at work. We seem to think that 20 people can work on a project together and all just magically decide where everything goes. That has been shown again and again to be a fallacy that we believe search will help us with. My argument -- from experience -- is that it does not, and that we need to go back to a world where we organise things, and that people are responsible for this organisation.