functions.php

<?php

/**
 * Exclude 'hidden' taxonomy from portfolio
 *
 */
function be_portfolio_query( $query ) {
  
  if( $query->is_main_query() && $query->is_post_type_archive( 'portfolio' ) && ! is_admin() ) {
    
    $tax_query = array(
        array(
            'taxonomy' => 'portfolio-category',
            'field'    => 'slug',
            'terms'    => array( 'hidden' ),
            'operator' => 'NOT IN',
        )
    );
    $query->set( 'tax_query', $tax_query );
  }
  
}
add_action( 'pre_get_posts', 'be_portfolio_query' );