I have had this problem since I began using Mountain Lion in December 2012. It only occurs on my Mac Mini that is always connected to external drives that have bootable volumes created using SuperDuper! Our 2011 13" MBP does not do this when its external drive is not connected. The problem goes away when the Mac Mini external drives aren't connected. I have used SD! since it was introduced and I have never had a serious problem with it until 10.8.
I contacted SuperDuper! tech support and Dave told me that it is a problem with 10.8 and not SuperDuper!. When I contacted Apple tech support I was informed that Time Machine is the only Apple-supported backup solution so Apple is not interested in the problem...
Since my contact with Apple I have just lived with the problem. But it is quite annoying to see a daily app update alert that I must manually scan each listing to find an app that needs to be updated.
I was planning on posting this on the Apple forum but I bumped into this forum today and I thought I'd see if anyone has a fix for this. At the very least I'd like to turn-off the app alerts. The Notifications preference pane doesn't have an option for disabling the alerts but I assume that there is a terminal command that will do the trick. But what I would really like is a way to make the app update notifications useful!