If you use the right-click option to play a folder which has (for example) three subfolders, then instead of lining up the songs from three subfolders, VLC lines up the name of the folder, instead of the individual songs from those subfolders.
Then, the Shuffle mode may play the same song twice before playing songs that were not played yet! That is not how Shuffle mode is supposed to work:
It is supposed to play each song once, randomly until all songs are played. Same song should not be played in shuffle mode, shuffle mode should play all the songs in random order, WITHOUT ever playing the same song twice in shuffle mode.
I also think that the Shuffle mode is not playing songs from within the subfolders because VLC Playlist lists subfolder names, not contents of those subfolders. But further testing is needed on that.