Hi,
You're missing something yes.
The product_id you had before for the main product is not deleted.
But yes, a product_id is added, one for each variant.
And what is referenced in the hikashop_order_product table's product_id column is the product_id of the variant of the product.
But fear not, in the hikashop_product, you have the product_parent_id column which points to the product_id of the main product of the variant.
So if you want to write a MySQL query where you have a condition on the product_id, it's totally possible. You just need to make your query a bit more complex by adding a join on the hikashop_product table to take into account the product_parent_id.