I’m answering this old question because I didn’t find anything better.
WordPress 5.9 wp-admin\options.php line 165 checks database version (when WP was originally installed) against a number to show or not those options.
if ( get_site_option( 'initial_db_version' ) < 32453 ) {
$allowed_options['writing'][] = 'use_smilies';
$allowed_options['writing'][] = 'use_balanceTags';
}
Not actually a solution, but maybe it’s useful to understand why those options are missing, my initial guess is that those are not needed when the database already support emojis natively (utf8mb4).