I made the change and the fix seems to work. In build_root_map() I replaced the sql statement formation with the code from the function that builds the individual sitemaps. Test on my dev system, and on a production site http://www.sparkle-gear.com.
In function build_root_map replace
$query = $wpdb->prepare( "SELECT COUNT(ID) FROM $wpdb->posts WHERE post_type = '%s' AND post_status IN ('publish','inherit')", $post_type );
$count = $wpdb->get_var( $query );
with
$where_filter = '';
$where_filter = apply_filters( 'wpseo_typecount_where', $where_filter, $post_type );
$query = $wpdb->prepare( "SELECT COUNT(ID) FROM $wpdb->posts {$join_filter} WHERE post_status IN ('publish','inherit') AND post_password = '' AND post_type = %s " . $where_filter, $post_type );