Workflows allow the use of notification content records without the need for a notification requirement record. Unfortunately, it is difficult to find where these notification content records are referenced, making it difficult to determine what may be sending them in error if the customized development is not well documented. Even in the case of as-delivered notification content, it can be difficult to find where they are used.
For example, TRIRIGA003 is a notification content record that notifies an individual of an assignment via email. If you do not want users to get these emails, you have to hunt down the workflow where the notification content record is referenced, and determine whether or not to create a customized version of the workflow and retire the original.
I have created a request for enhancement (RFE) for this functionality: Where Used for Notification Content Records (RFE ID 94293).