It's in the function loadOrderNotification of the file administrator/components/com_hikashop/classes/order.php where the email is loaded.
Normally, the override is done automatically in joomla 1.6 and manually on 1.5 in the file amdinistrator/components/com_hikashop/helpers/helper.php :
$lang =& JFactory::getLanguage();
$override_path = JLanguage::getLanguagePath(JPATH_ROOT).DS.'overrides'.DS.$lang->getTag().'.override.ini';
if(version_compare(JVERSION,'1.6','=')&&$app->isAdmin() && file_exists($override_path)){
$lang->override = $lang->parse($override_path);
}
$lang->load(HIKASHOP_COMPONENT,JPATH_SITE);
if(version_compare(JVERSION,'1.6','<') && file_exists($override_path)){
$lang->_load($override_path,'override');
}
However, on joomla 1.6.1 and higher, the override system cannot be called from the back end. So all the backend and the emails sent from the back end cannot use the overridden translations.