What is the difference between the two functions? When should one be used instead of the other?


The functions are essentially opposites.

The only real difference is the user_is_anonymous() function has an additional check for $GLOBALS['menu_admin'] to allow menu admins to be able to administer menu links that are visible to anonymous users only.

It's used by drupal_valid_path() as well as the menu_overview_form() function:

function drupal_valid_path($path, $dynamic_allowed = FALSE) {
  global $menu_admin;
  // We indicate that a menu administrator is running the menu access check.
  $menu_admin = TRUE;
  if ($path == '<front>' || url_is_external($path)) {
    $item = array('access' => TRUE);
  elseif ($dynamic_allowed && preg_match('/\/\%/', $path)) {
    // Path is dynamic (ie 'user/%'), so check directly against menu_router table.
    if ($item = db_query("SELECT * FROM {menu_router} where path = :path", array(':path' => $path))->fetchAssoc()) {
      $item['link_path']  = $form_item['link_path'];
      $item['link_title'] = $form_item['link_title'];
      $item['external']   = FALSE;
      $item['options'] = '';
  else {
    $item = menu_get_item($path);
  $menu_admin = FALSE;
  return $item && $item['access'];
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