Let me make sure I have what you want to do correct. You want to hide all system updates from showing to the user in the App store, and for showing a notification in the top right (notification center) to them?
That is kind of a two factor item. You want to
1 - Set the system preference for Software Update (aka App Store in newer OS X) to have the "automatically check for updates" uncheck
2 - Make it so the user can't recheck that box
(as a side note, doing this will still allow the FileWave client and Admin's software update UI to see what updates the client needs, and to send it new updates. This is a great way to remove the burden of updates from the end-user)
1 - We need to run several default writes commands to un-check those boxes in the software Update window as well as tell software update to stop checking, and we would end up with a script that looks something like :