I call BS, App certs do not have any use whatsoever in the TCP stack. I'm sure people had problems, but it wasn't due to this.
If the app in question is a VPN app, then it's entirely possible that they literally could not connect to the Internet with the app disabled.
Alternatively what's meant is that they couldn't connect to the Internet at the time and were therefore locked out of their legitimately purchased apps until whatever time they could connect to the Internet. Not everyone has a 24/7 Internet connection. (Seems unlikely for someone who can afford the huge expense of an Apple product, but whatever.)
I call BS on that too. The app settings are in a text file in the user directories, you can go and open them in your favorite text editor right now. Re-installing an app does not overwrite these settings, which is *the whole reason* they're done this way. It is possible that app did that, but that's a bug in the app and has nothing to do with certs.
I could have sworn part of removing an app via the App Store (or via Launchboard or whatever it's called) is that it deletes all the app's data as part of the process, just like it does under iOS.