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