It's important to remember that cPanel and Fantastico are two different products by two different companies.
At cPanel, we do periodically update the scripts which have a "one-click install" through cPanel and can be managed through WHM. Server administrators can even push these upgrades to all their users if they desire, but that would overwrite any customizations individual users may have made to their installations of said scripts.
Note this is completely independent of the features of the Fantastico interface.
cPanel Technical Product Specialist