Yes, I think this may be why it's been removed but, if so, it's missing the point.
Pre-2.0.x one could disable email notifications (which were the primary notification method if we disregard Messaging pop-ups) easily in one's profile.
This was great for test accounts and holiday absences etc.
If our assumptions above are correct the user now has to re-configure their Messaging settings page. This overhead isn't an improvement for normal users.
If the setting isn't to re-appear in the profile a "Suspend messaging" setting on the new page would be a handy addition IMO.