Hi,
First, you have the "Update the product stock on confirmed status" setting in the HikaShop configuration.
If turned off, the quantity will change in the product the moment the order is created.
If turned on, the quantity will change in the product when the order status changes to one of the statuses enabled under the "invoice" column of the System>Order statuses.
So I suppose that this setting must be turned on on your website and the "confirmed" status must be disabled under the "invoice" column of the System>Order statuses and that's why the stock is not being updated.
Please check these settings.