Hi,
You're wrong. If you set a canonical URL in your products, the canonical URL will also be provided in the sitemap.
We actually have a plugin for the major sitemap extensions for Joomla:
www.hikashop.com/support/documentation/8...ation-with-xmap.html
It will add the canonical URL of the products / categories if it's filled in.
Plus, even if we were not doing this, when the search engine gets the other URL to the product page in the XML sitemap, it will load that URL and in the meta tags of that page, he will find the canonical URL that you specified in the product and will use it for the referencing and will ignore the one in your sitemap. Thus, it wouldn't impact your SEO even if that were to be the case.
I don't understand what you mean by "all the item menus are for the brands". When you create menu items via the Joomla menu manager, you can select the type. If you select "HikaShop categories listing", you'll get by default a listing of the categories of your shop when accessing that menu item.