Being the curious sort, I just powered up my PB360 and used the "Move to Folder" function to *create* a nested folder destination 12 levels deep and move a test file there. It worked.
I'm fairly certain there is no arbitrary limit on how deep you can go since it's a standard FAT32 file system and the PB360 is LINUX-based.
Now, there *will* be a limit to the length of the resultant *path-name*. I'm not sure what the LINUX path-length limits are these days (256 characters? More? Less?) but I doubt that will impinge on a reasonable organization system. But if you really want to give full-sentence names to your folders you might run into a wall at some point.