Q: how to stop gatekeeper from repeatedly asking to open vlc

Gatekeeper doesn't ask if you want to Open an app, just if you want to install it. If it is asking if you are sure you want to open this program downloaded from the Internet, that is the Quarantine system.

About the "Are you sure you want to open it?" alert (File Quarantine / Known Malware Detection) in OS X - Apple Support

I think there is a database that updates the quarantined items as I have quite a few with the Quarantine extended attribute, but they don't complain.

You can try removing the attribute and see what happens. Copy and paste this into Terminal. If you don't have VLC in your Applications folder, then let me know where it is as this won't work if you've put it somewhere else:

xattr -dr com.apple.quarantine /Applications/VLC.app/