the relevant code is SendNotification in Library\Services\Social\Notifications\NotificationsControllerImpl.cs -however the problem is that this code simply creates the notifications - these show up in the users message centre, but there is a seperate function (Library\Services\Social\Messaging\Scheduler\CoreMessagingScheduler.cs) which acts as a message scheduler which picks up and sends out emails (a notification is simply a custom message)

Perhaps the easiest thing to do would be to add code to the SendNotification section that would update the messagerecipient to be marked as sent, so the scheduler will then ignore it -you can do that via a call such as this (if you get the messageid first) or by directly updating via the MessageRecipeient class

InternalMessagingController.Instance.MarkMessageAsDispatched(objMessage.MessageID, objMessage.RecipientID);