Sorry this is proving so problematic... can you just clarify - is the delete option in WMP absent on any track or just certain ones? Its not possible to delete a track from WMP that has been moved or altered in 'explorer' but any other track should have the 'delete' (either from library only - or from library and computer) - You don't have a 'hide' option in WMP - just in the folders.
I think maybe you should look to making sure your music photos etc. are backed up off the pc just in case there's a system problem going on here.