you can also store it like yyyy-mm-dd and and use
$date_array = explode( '-', $date_string );
to make it into an easy to manage array. or even better change it into a unix timestamp with
$unix_time = strtotime( $date_string );
php loves to work with unix time stamps, it’s the native format.
and when you’re ready to store the value again in the meta field use this to get the proper format again
$date_string = date( 'Y-m-d', $unix_time );