The solution you propose is a good one, but it might not work on certain players. If I understand the Nomad file structure correctly, files are renamed to a unique "index number" by the Nomad driver upon transfer. The Nomad builds a database of artist/album/genre information during transfer, and the database uses the index number to access the files. This is why you can't just drag-and-drop files on a Nomad like it was a USB drive.
Ostensibly, this database/index structure makes the Nomad faster at browsing a library than a player that has to read the tags from the files in real time.
Now, I'm no programmer, but I infer from this that the Nomad driver doesn't let the programmer set the filename on the device directly. I infer that the programmer tells the Nomad driver what the Album, Artist, Genre, Year, and other tags are for the file, but he's got no control over the actual name or structure of music files. To make matters worse, I don't think Nomad supports custom tags of any sort, so you'd be stuck re-using an existing tag for the MC index.
Nomad works around this by detecting duplicates when Album, Artist, and Title are the same for any two tracks. Unfortunately, filename doesn't matter because filename on the player is controlled by the driver.
But if I'm wrong, and you _CAN_ set the file name on the Nomad, then this is a great idea.