Hi,
The count is done based on the link between the elements in the hikashop_product_category table.
Through the interface of HikaShop, it's normally impossible to add entries in that table for variants (since variants don't have a "categories" setting).
However, if there was some custom plugin, or maybe some weird mass action, or maybe some wrongly configured CSV import, it might be possible to have such entry in the hikashop_product_category table, which would explain why variants are counted.
But again, normally, it shouldn't happen.
Could you check the entries in that table through your phpmyadmin ?