How to enable ckeditor in the emails templates at admin/config/people/accounts?
Create custom module for Drupal 7;
Add below code to your module;
replace all MODULENAME in code to your module name;
clear cache;
refresh /admin/config/people/accounts page


For all textarea fields there's text selector appear - you should select format, where ckeditor attached:

/**
 * Implements hook_form_FORM_ID_alter() for user settings page.
 */
function MODULENAME_form_user_admin_settings_alter(&amp;$form, &amp;$form_state, $form_id) {
  _MODULENAME_form_user_admin_settings_elements($form);
}

/**
 * Scan through elements.
 */
function _MODULENAME_form_user_admin_settings_elements(&amp;$elements) {
  // Recurse through all children.
  foreach (element_children($elements) as $key) {
    if (isset($elements[$key]) &amp;&amp; $elements[$key]) {
      if (isset($elements[$key]['#type']) &amp;&amp; ($elements[$key]['#type'] == 'textarea')) {
        $elements[$key]['#type'] = 'text_format'; 
      }
      else {
        _MODULENAME_form_user_admin_settings_elements($elements[$key]);
      }
    }
  }
}



be warn, that placeholders signs [bla-bla:something] can be replaced by unicode symbols (&XXXX;), check before to show your client.
if you want add text format only for certain textarea use Devel module dpm function for seeking that element and setting next code $elements[CERTAIN_ARRAY_PATH2ELEMENT]['#type'] = 'text_format'; without scanning through all elements.