remove_action in plugin file

by

Make sure you remove the action after the theme has added it. And use the same priority.

A rather safe way is using the same action you want to clean up:

add_action( 'admin_notices', 'remove_woothemes_updater_notice', 0 );

function remove_woothemes_updater_notice()
{
    remove_action( 'admin_notices', 'woothemes_updater_notice' );
}