Hi,
i have problem in cart with short link if disable Use full category tree for product links link is /cart/product instead of /category/product, if enable all ok link is /category/subcategory/product.
For seo is better link /category/product or we use the best option /eshop/product.
Do you use override template?
The option below creates more work for you
You can get what you want by creating a "non visible" joomla menu item for every category and make that joomla link the single VMcategory link
Regardless of how deep your subcategories go - you will then see links:
domain/category
domain/category/product
Now let's not deal with seo but real bug if disable Use full category tree for product links, link to product in cart links to cart page not to product page.