Hi,
The goal of the manufacturer / brand feature is to be able to access products from the same manufacturer / brand. So, on the product page, it has to add a link to the manufacturer / brand to see the other products, and thus it is normal this URL is available and indexed.
If you're only using manufacturers / brands for the filtering on the product pages, then you could actually do the same with a custom product field where each choice of the custom field would be a manufacturer / brand. And the custom field wouldn't have a link to access the products of the same manufacturer / brand on the frontend.
If you wish to do so, you'll probably want to use mass actions to auto fill the custom field in the products based on the brand selected so that you don't have to edit the products one by one.
Now, you're saying "**unpublish some categories** and instead link to them via Joomla menu items,".If I read between your lines, it seems that for each manufacturer, you've created a menu item to be able to display its products. In that case, you don't need to unpublish them. Leave them published, and simply enter the URL of that menu item in the "canonical URL" of the brand / manufacturer. That way, the indexed page for the brand will be URL you've created. Now, you'll still have the "/menu/category/manufacturer" URL on the product page but it won't be indexed.