How to sort by meta value num, but ignore zero value?

You can use a meta_query in your WP_Query

$args = array(
    'post_type'  => 'company',
    'meta_query' => array(
        array(
            'key' => 'service_XXXX_price',
            'value' => '0',
            'compare' => '!=',
        ),
    ),
);
$company_query = new WP_Query( $args );

You can find more infos about the meta querys in the codex: https://codex.wordpress.org/Class_Reference/WP_Query