It looks like toggling the notification setting from the drop-down menu only works until the following boot.
Such notifications are handled by the following script:
/usr/share/nvpmodel_indicator/nvpmodel_indicator.py
Setting the notify_disable variable in said script seems to be a permanent solution:
sudo sed -i 's/notify_disable = False/notify_disable = True/g' /usr/share/nvpmodel_indicator/nvpmodel_indicator.py