If you have a look at https://github.com/markn86/moodle/commit/0f38e629708ee4ff1d2d#diff-70474039f34732254a0125a4d020c19aR96 you can see that it marks the notification as read if it finds it, but that ID could be the ID of a message (which may also exist as an ID for a notification) which would then cause the notification to be marked falsely.

Follow-up - I now think this behaviour shouldn't exist at all. Just because a notification/message is sent via email does not mean it will get read, so we shouldnt blindly mark it as read in Moodle.