Of course, the obvious drawback is that Windows would have no good way to have tracks be in multiple playlists. Or maybe it could have understood both hard links, soft links, and Windows shortcuts and presented them properly to whatever host-type it was attached to.
You could always use playlist files (.m3u or whatever) instead of directories. I don't know what actually happens at the structure level when you mount a FAT filesystem under Unix and make a symlink on it -- I bet it doesn't make a .lnk file -- but yes, it'd certainly be helpful for a mass-storage player to understand whatever it is.

Peter