Hi,
The issue is not really a Joomla or a HikaShop issue.
It stems from how the routing of URLs is done in Joomla.
When you generate a SEF URL, you need to add a Itemid parameter in the URL. That way, when the router get the URL to display the page later on, it knows which menu item to use.
There is no information in the products on which menu item is used to display it. You could configure many menu items to reach the same product page.
And the search plugin can guess which menu item to use, but it doesn't know which one YOU want it to use. So it has to pick one.
You can potentially select one menu item in the search plugin settings, but then all the product results will use that menu item.
So if you want that the results have the URL of a menu item different for different products there is only one solution left:
You need to activate the "force canonical URLs on listings" setting of the HikaShop configuration and configure a canonical URL in each product.
A canonical URL is the main URL you want the system to use. It's important for SEO so you should have it filled in regardless.
Note that the "force canonical URLs on listings" has the possibility to generate them for you. If you choose that, just browse your shop proudcts listings the way you want the URLs to be and they will be filled in.
Once filled, the search plugin will use the canonical URLs and thus you'll get the links you want.