I figured these messages would annoy people, what with the amount of updates lately and the many times this bug has been supposedly fixed, but I had no idea how many. Personally, I don’t get the messages at all, I mean what if every plugin had them? It would be a mess of messages on every update. So in the spirit of peaceful site administration, I’ll pass along this snippet I’ve found somewhere a while back. Add it to your theme’s functions.php file and Yoast SEO will update just as silently as your other plugins.
// disable yoast seo nag messages
if ( class_exists( 'Yoast_Notification_Center' ) ) {
remove_action( 'admin_notices', array( Yoast_Notification_Center::get(), 'display_notifications' ) );
remove_action( 'all_admin_notices', array( Yoast_Notification_Center::get(), 'display_notifications' ) );
}