I dont think there is a direct way to disable and re-enable the notifications.
However you could write two scripts which you could have on your desktop or a dock such as awn/docky etc. The scripts would remove the execute permission from the executable that is run to display the notification. You also need to kill the notification process that is running.
one script - lets call it "disableNotify" could have the commands
sudo chmod -x /usr/lib/notify-osd/notify-osd
the other script - lets call it "enableNotify" could have the commands
sudo chmod +x /usr/lib/notify-osd/notify-osd
Create each script as a text file in Text Editor
Give the script execute rights i.e.
chmod +x enableNotify
chmod +x disableNotify
The scripts will obviously prompt you for your password since it uses "sudo". There are ways to prevent this but that is perhaps worth another question.