Hi,
There is no brand link on the products listing pages. It's only on the product pages. And on the product pages, the brand link already uses the canonical URL of the brand if provided.
The link is done with that code:
echo JText::_('MANUFACTURER').': '.'<a href="'.hikashop_contentLink('category&task=listing&cid='.$manufacturer->category_id.'&name='.$manufacturer->alias.'&Itemid='.$Itemid,$manufacturer).'">'.$manufacturer->category_name.'</a>';
I'm thinking that you customized your views with an old code where the brand link is generated with hikashop_completeLink instead of hikashop_contentLink and thus it doesn't take into account the canonical URL.