How to wrap a text with shortcode into php file?

You can use the load_value ACF filter:

function wpse0605_acf_load_field( $field ) {
    $field = '[box]' . $field . '[/box]';
    return $field;
}

// acf/load_field/name={$field_name} - filter for a specific field based on its name
add_filter('acf/load_value/name=diorganwths_diagwnismou', 'wpse0605_acf_load_field');
add_filter('acf/load_value/name=apaitei_logariasmo_facebook', 'wpse0605_acf_load_field');

The code can go into the theme’s functions.php, or inside a plugin constructor.