After reviewing the fact that no new notifications were provided by the SCCM 2012 Client for applications beeing deployed a quest for the right log-file to locate the root-cause, it was a great relief to identify all notifications beeing processed in a single log-file.
SCNotify_DOMAIN@USERNAME_1.log presents a complete history of what the user has been presented with. However, this was shown;
Notifications are globally suppressed, this event will not be processed by NotifyObjectInstanceBase (Microsoft.SoftwareCenter.Client.Notification.NotifyObjectInstanceBase at IsKnownEvent)
It seems that the Computer Agent settings has a setting which doesn’t directly reveal its impact, however the documentation clearly states that it will disable notifications.
Additional software manages the deployment of applications and software updates
Enable this option only if one of the following conditions apply:
You use a vendor solution that requires this setting to be enabled.
You use the System Center 2012 Configuration Manager software development kit (SDK) to manage client agent notifications and the installation of applications and software updates.
It seems that reboot notifications are not impacted by this as it requires a few more tricks provided by Microsoft to suppress them.