I believe that only the listed MimeType= in an apps .desktop will be changed (set as default or added thru SS
So in that regard not all mimetypes would be changed to vlc, though in your case none are.
What is on the MimeType= line in vlc's .desktop?
Do you have a vlc.desktop anywhere else like /usr/local/share/applications or ~/.local/share/applications ?
(the other mystery is why the r. click > properties > open with on any video file type > pick Vlc media player > set as default doesn't work
(also just for info
apt-cache policy vlc