Further reply from support:
"About your query, when customers receive payment emails, each email contains a unique payment link assigned to that particular customer, even if there are duplicate invoice numbers. This system ensures that each customer is directed to their specific invoice for payment. Consequently, customers will not encounter issues when accessing and paying the correct invoice online, regardless of any duplicated invoice numbers."
That's a relief. Could still be an issue I imagine, if people wanted to pay by bpay since they wouldn't have unique reference numbers but fortunately we have that option turned off.