Hello,
If you take a look at the HikaShop "user account" plugin, you will see:
if(version_compare(JVERSION, '1.6', '<')) {
$url = JRoute::_('index.php?option=com_user&view=user&task=edit'.$url_itemid);
} else {
$url = JRoute::_('index.php?option=com_users&view=profile&layout=edit'.$url_itemid);
}
The parameter "url itemid" is something you can configure in the plugin ; now if you have provided a wrong Joomla menu, it would explain why your URL are wrong.
Otherwise, i'm afraid that the problem is not related to HikaShop at all but it coming from a plugin or component related to the SEF.
Because HikaShop is using the Joomla router system in order to generate that link ; it can't be responsible of the final URL, specially if that link to pointing to another component (so it's not related to the HikaShop router file).
Regards,