Exclude Woocommerce product categories

Yes, you can. It happens exactly as it does in the WP default search, using taxonomy parameters. See documentation here. For example, to exclude product categories 5 and 7, you can use:

add_filter( 'relevanssi_modify_wp_query', function( $query ) {
  $tax_query = array(
    array(
      'taxonomy' => 'product_cat',
      'terms'    => array( 5, 7 ),
      'operator' => 'NOT IN',
      'field'    => 'term_id',
    )
  );
  $query->set( 'tax_query', $tax_query );
  return $query;
} );