In GNOME 3.12 the updates plugin has been removed from gnome-settings-daemon, now the updates are supposed to be handled by gnome-software.
I don't use gnome-software so I am not sure this will work, but you can prevent gnome-software from starting at login, this may well stop the updates notifications. Copy /etc/xdg/autostart/gnome-software-service.desktop to ~/.config/autostart/ (create ~/.config/autostart/ if it doesn't exist), then edit ~/.config/autostart/gnome-software-service.desktop and add this line to it:
Code:
X-GNOME-Autostart-enabled=false
then log out -> log in.