Hi,
When Joomla generates a SEF URL from the non SEF URL that an extension gives it, it looks at the Itemid parameter of the non SEF URL, it removes it from the SEF URL. This Itemid parameter contains the id of the destination menu item. And instead of that parameter, it add either component/XXX/ where XXX is the name of the destination component, or YYY/ where YYY is alias of the destination menu item. It will use YYY/ if the Itemid parameter is specified and that its menu item is of one of the types of the destination component. Otherwise, it has to add component/XXX/ so the the SEF system can display properly the page with the correct component upon arrival on the page of the link.
So this means that if you have component/XXX/ in the generated URLs of a module, either its destination "menu" is not specified, or it is specified with a menu item which is of a wrong type.
It's actually the same principles for any extension, HikaShop or not.
If you have the URL:
component/hikashop/product-title?Itemid=0
it means that you didn't select any menu, or a menu that has been trashed, deleted, etc in the "menu" setting of your module (that you can find when you edit it via the menu Display>Content modules).
Now regarding content duplication, HikaShop has canonical URL fields for products/categories that you can fill to avoid that. The simplest is to set the "force canonical URLs on listings" setting of the HikaShop configuration to generate the canonical URLs and then look at your normal products listings once (so that the system fill them in). And then the canonical URLs should be filled and you'll get the links you want in the related products module.