Hey Matthew,
We've got the same issue here, we use Shipwire and they have shipping notifications as well. I have deactivated Shipwires, but now there is an issue with the Shopify notification (tracking). I guess Shopify doesn't recognize Purilator and TNT and it attaches their tracking #s to a FedEx URL, which obviously doesn't work. Either you guys need to add the other shippers to resolve the tracking glitch or there needs to be a way to disable the notification.
Regards,
-Brett