You can add following code in your theme’s (child theme’s if you are using) functions.php. It will hide those users from autosuggestion who unchecked “Allow others to send me messages?” in their settings.

add_filter( 'fep_filter_rest_users_args', function( $args, $for, $q, $x ) {
	$args['meta_query'] = [
		'relation' => 'OR',
		[
			'key' => 'FEP_user_options',
			'value' =>  's:14:"allow_messages";s:1:"1";',
			'compare' => 'LIKE',
		],
		[
			'key' => 'FEP_user_options',
			'compare' => 'NOT EXISTS',
		]
	];
	return $args;
}, 10, 4 );