Almost everything is deleted by this file:
https://github.com/woothemes/woocommerce/blob/master/uninstall.php
We delete the products, but seems that need to delete terms too.
I started a thread about it, so we can think about include terms to be deleted: https://github.com/woothemes/woocommerce/issues/10494
When I reinstall the plugin the categories remain with a product count next to it...
That count are salved on cache I think, if you create a new product check the category will reset the number too.