Как не отображать в Views фильтре с использованием модуля SHS термины, к которым не прикреплены ноды

Попробуйте
hook_shs_term_get_children_alter() и
taxonomy_select_nodes()
Пример

<?php

/**
 * Alter the list of terms within a level of the term hierarchy.
 *
 * @param array $terms
 *   List of terms displayed to the user (single hierarchy level).
 * @param array $alter_options
 *   - vid: ID of vocabulary or field name
 *   - parent: ID of parent term
 *   - settings: Additional settings (for example "language", etc.,)
 */

function YOUR_MODULE_shs_term_get_children_alter(array &$terms, array &$alter_options) {
  $vid = $alter_options['vid'];
  $lang = $alter_options['settings']['language']->language;
  $array = &$terms[$vid][$lang];

  foreach($array as &$terms) {
    foreach($terms as $tid => $name) {
      $child_related_with_node = FALSE;
      $nodes = taxonomy_select_nodes($tid, FALSE);
      if (count($nodes) != 0) {
        continue;
      }
      else {
        $children = taxonomy_get_children_all($tid, $vid);
        foreach($children as $term) {
          $nodes = taxonomy_select_nodes($term->tid, FALSE);
          if (count($nodes) != 0) {
            $child_related_with_node = TRUE;
            break;
          }
        }
        if ($child_related_with_node == FALSE) {
          unset($terms[$tid]);
        }
      }
    }
  }
}

function taxonomy_get_children_all($tid, $vid){
  $c = taxonomy_get_children($tid, $vid);
  $result = array();
  foreach ($c as $t => $d){
    $result[$t] = $d;
    $below = taxonomy_get_children_all($t, $vid);
    if (!empty($below)) {
      foreach ($below as $nt => $nd){
        $result[$nt] = $nd;
      }
    }
  }
  return $result;
}