It could potentially be that you edited the "show" file of the view "product" before updating HikaShop and because of that, you didn't get the modifications for canonical URLs.
In that case, you would have to add the code in it via the menu Display->Views yourself:
Code:
<?php
if(isset($this->element->product_canonical) && !empty($this->element->product_canonical)){
$parsedCanonical = parse_url($this->element->product_canonical);
$parsedCurrent = parse_url(JURI::base());
if(!isset($parsedCanonical['query']))
$endUrl = $parsedCanonical['path'];
else
$endUrl = $parsedCanonical['path'].'?'.$parsedCanonical['query'];
$canonicalUrl = $parsedCurrent['scheme'].'://'.$parsedCurrent['host'].$endUrl;
$doc =& JFactory::getDocument();
$doc->addCustomTag( '<link rel="canonical" href="'.$canonicalUrl.'" />' );
}
?>
or remove your customization.
