Hi,
You're mixing several things here.
1. The component/hikashop part of URLs. This will be added automatically by Joomla's SEF system when the Itemid parameter is missing in the URLs or if the component of the menu item is a different component than the component necessary to the display of the page.
For example, if you're trying to SEF a URL like this: index.php?option=com_users&view=registration&Itemid=18 where 18 is the id of a menu item of the type hikashop products listing (or any other component than com_users), you'll have component/users added at the beginning by the Joomla SEF system.
This problem will often happen with HikaShop when you have configured a products/categories listing module without selecting a Hikashop menu item in the "menu" setting of the module (via the Display>Content modules menu). That's what is used to set teh Itemid. Without it, Joomla will often add component/hikashop at the beginning of the SEFed URLs.
So that problem is merely a setting issue.
2. When you configure your website, you'll be able to creating modules and menus generating different URLs for the same content (because they use different Itemid parameters, etc). The will hinder SEO as crawlers will flag your URLs as duplicate content.
To avoid that, we added a canonical URL field in products and categories so that you can enter there the main URL you want to use among all these URLs. Of course, if you change the alias of a product/category, you also need to change it in the canonical URL if you want to keep the consistency since the alias is used by the system to understand the which product to display when the link is used.
3. To make it easier for merchants to configure their products, we've added the "force canonical URL on listings" setting of the HikaShop configuration. It can either be turned off and the canonical URL will only be used be crawlers as the main URL of a product/category for SEO purposes if specified, or it can be activated. If activated, the canonical URL will replace the normally dynamically generated URL and thus, it will break the links to the products pages if the links you have in the "canonical URL" fields are not valid anymore (they should be fixed in that case). Finally, it's also possible to configure that option to have HikaShop use the canonical URL if provided, or fill it with the first generated URL it has to generate for the product (and then use it all the time). That's a great time saver when you want the system to fill all the canonical URLs for you but if you later on change the aliases, or the menu structure, it's up to you to fix the canonical URLs or the links to the products won't work anymore.