$banner_subtitle = get_post_meta( $post_id, 'header_section_meta', true );
if (!empty($banner_subtitle['banner_subtitle'])) {
echo $banner_subtitle['banner_subtitle'];
}
or as a ternary
$banner_subtitle = get_post_meta( $post_id, 'header_section_meta', true );
echo !empty($banner_subtitle['banner_subtitle']) ? $banner_subtitle['banner_subtitle'] : '';