SOLVED! If you have "Show all folders" enabled in the Windows Explorer "folder options" settings, then the Library properties "Show in Navigation Pane" is automatically checked and disabled. Once you uncheck the "Show all folders" in the Explorer Folder options, the property then re-appears in...
Actually - it's not a question so much of removing them.... it's the issue of the "shown in navigation pane" option is not actually "clickable" when it should be.... I do use the Libraries feature (for custom ones) - but I don't want to see the Default libraries (music, videos, pictures) there...