I've been thinking about this project and came across a different approach. Instead of implementing unionfs-like view inside the file browser, I would be using the database for "Merged folder view". This project would involve improving tagnavi capabilities to allow such hierarchical view of the folders. Since it would be read-only, there would be no mess with file and folders locations, also I guess duplicated files wouldn't cause problems.
And since this project is probably easier, it would also focus on implementing some other useful features to tagnavi. Some things I missed on it were, for instance, composing logical operators like OR (as sideral mentioned) and basic regexp support. Let me know what you think of this. Marcelo