Functions, which aren't wrapped inside
functions_exists() calls, are not meant to be pluggable. If you're searching for extensions, then use filters or hooks - in case there're some.
As you can read in the phpDocBlock:
Ensure that the welcome message is not empty. Currently unused.
So this filter won't work.
I'm no MU expert, but maybe you can make use of the following filter:
__( "To activate your blog, please click the following link:\n\n%s\n\nAfter you activate, you will receive *another email* with your login.\n\nAfter you activate, you can visit your site here:\n\n%s" ),
$domain, $path, $title, $user, $user_email, $key, $meta
You'd call it like this:
function wpse56797_signup_blog_notification_email( $message, $domain, $path, $title, $user, $user_email, $key, $meta )
$message = 'Your custom notification';
add_filter( 'wpmu_signup_blog_notification_email', 'wpse56797_signup_blog_notification_email', 10, 8 );