Hi,
Well, it depends of the status of the order.
You could create a specific order status to use for such orders and exclude these orders from the statistics ( and create new statistics to count these orders if necessary)
Regarding have refund invoices, I think it would make more sense to have a "refund invoice" option so that when it's activated, HikaShop would create a second "invoice number" for the order when the order status changes to "refunded", and you would then have a "refund invoice" button on the order edition screen to be able to print the refund invoice, using the refund invoice number and the amounts in negative.
What do you think about this ?