App-V: VLC 2.0
Disabling update notifications appears to be held in the file located at:
Thats a file not a folder. Simple way to capture config for this app is one of two options, either run the install/app and configure it then capture this folder and copy it to the sequencer when you sequence the app, or simple launch VLC after it installs (while still in the monitor phase) and configure it. Depending on your exclusions you may have to adjust them for the sequencer to pick this folder up, but that depends entirely on what changes you have made (it should pick it up fine by default in 4.6 SP1).
Note: This version launches MUCH faster in App-V than 1.x did.