I realize that's the way it is designed, I'm just saying that I don't like it much myself.
I would much rather see 5 on the notification if there are 5 different updates that can be installed on their own. As it is, my App Store icon has had the 1 on it for about a month, maybe longer because I don't really remember ..... and I have updated iTunes, the system update to 10.8.4, one of the RAW camera updates and the AirPort utility update. There is an update for my printer, a MacBook firmware update and I think one other item in the App Store when I click on More to reveal everything. I'm not at home to check for sure, but I know that the printer software and the firmware update have not been installed.
I am not the sharpest knife in the drawer, but by my count, that's 3 updates - 2 at the very least - and not 1 like the notification tells me.