Stubs for old notifications are retained to sync deletes across devices. There is no need for these events to be replayed on brand new devices, but at the moment the initial sync is no different from any other, so deletes are not ignored. The whole notifications isn't downloaded or stored on your iPad, just the ID along with an indicator that the notification has been deleted.
The correct thing to do would be to only get the minimal set of current notifications, but this currently isn't implemented.
Hope that clears things up.
Jon