So you are going to the NAS in Finder, and telling it to open a mp3 file with iTunes? Normally if you do that iTunes will copy the file to the location you have designated as the place to store media files, then add the listing to the iTunes database, rewriting the database and recalculating any smart playlists you have. From your NAS folder structure this is not the location of file on the NAS, but maybe you do have your media files being stored on the NAS too?
Or as I said before this could just be another un-explainable problem with iTunes and a NAS. If you ask your NAS manufacturer they will say it is iTunes, if you ask Apple they will say it is a problem with the NAS software.
Another issue I wonder is wi-fi. Can you hardwire this to just exclude that as a possible source of issue?