While this is not a Raspberry Pi specific question but rather a Linux/Unix command line question here is how I do it:
find <folder> -type d -empty -delete
in words: Find all file system entries in <folder> of type directory which is empty and go delete it.
ntfs-3g has a limited support for journal: it will try to clear the existing entries before mounting (thus allowing you to mount a partition which was not unmounted cleanly), but it will not create new journal entries when you write on an already mounted volume.
One more reason to always unmount NTFS disks before disconnecting them from the RPi.