Hi,
It's not the "root category" you see in the URL, it's the alias of a menu item on your website taken randomly by the smart search plugin during the indexing so that the URLs can be valid.
And unfortunately, we can't use the canonical URL because Joomla requires us to provide the non SEFed URL when indexing the elements.
But I agree with you that it would be nice if the smart search plugin could automatically search for the menu item linked to the main category of the product in order to provide a nicer URL to the smart search system. We'll look at improving this for the next version of HikaShop. Thanks for your feedback.