I'm having this same problem. Music files on an external drive (which is quite large) and Younity isn't seeing them, although it did find everything on the local drive. I currently have the search location down to just one band folder for testing and ran the scan overnight with no results.
I take it back, the material from my test scan of just one folder on my external drive DID show up after about 20 hours. I've just set it to scan the whole thing and we'll see what happens but at this rate the scan of the external drive will take...months? It would be nice in the future to see some feedback about what is scanning and maybe even an eta.