How to alter auto-complete exposed filter programmatically?
Here is a possible answer to this problem.
First of all, a litte visual.  



To get this working you need the following:


Configure your View to display the exposed taxonomy filter as a dropdown. autcomplete will not work because you cannot have multiple entries with the same key in the generated JSON array.
Optional: Install and configure the Chosen module [https://www.drupal.org/project/chosen] to get your dropdown to render nicely and offer autocomplete options.


You will also need this JS library for Chosen to work => [https://github.com/harvesthq/chosen]

Optional: You can finally use some custom code for formatting the presentation of your list, here is a sample minimal module that adds the special arrow that you see in the screenshot.



define('YOUR_CUSTOM_TAXONOMY_AUTOCOMPLETE_PATH', 'mycustompath/1');
define('YOUR_EXPOSED_FILTER_MACHINE_NAME', 'field_tags_tid');

/**
 * Implements hook_form_alter()
 */
function se_form_alter(&$form, &$form_state, $form_id) {
  if( $form_id == 'views_exposed_form' ){
    if(isset($form[YOUR_EXPOSED_FILTER_MACHINE_NAME]) && 
    $form[YOUR_EXPOSED_FILTER_MACHINE_NAME]['#type'] == 'select'){
      $form[YOUR_EXPOSED_FILTER_MACHINE_NAME]['#options'] = _custom_update_options_for_taxonomy($form[YOUR_EXPOSED_FILTER_MACHINE_NAME]['#options']);
    }
  }
}

/**
 * Function that update select options for taxonomy filter
 * 
 */
function _custom_update_options_for_taxonomy($options = array()) {
  $current_parent = '';
  foreach( $options as $i=>$option ) {
    if( is_int($i) && isset($option->option) && is_array($option->option) ) {
      $option_arr = $option->option;
      $tids = array_keys($option_arr);
      $tid = reset($tids);
      // is this a child of the previous parent
      if( strpos($option_arr[$tid], '-') === 0 && $current_parent != '') {
        $option_arr[$tid] = preg_replace('/^-/', ' ⤷ ', $option_arr[$tid]);
        $option->option = $option_arr;
      }
      // this is a parent node
      else {
        $current_parent = $option_arr[$tid];
      }
    }
  }
  return $options;
}


Hope this help some!