I had recently written a post on etsy kind of websites. i think a global header is needed for network stores so that uses can navigate through out the network with ease
of course each theme has its own headers/scripts/functions in header.php that cant change i think..
however a global header above the theme header would be very helpful exactly like the global footer plugin, but above the theme header.
there is already a plugin of that sort
http://wordpress.org/extend/plugins/wpms-global-content/ which i am using at the moment