The zero cheque (even though No Cheque is actually printed) comes into play when an employee has received Advances which (or the Deductions) exceed their Net Income. In these situations they want to provide the employee with a printout of the payroll detail (earnings & deductions), while the balance (if the cheque does not work out to zero) to be applied back the the Advance account or to an AR account.
An auditor would not have a problem with a so called zero cheque, especially since it does reflect that the employee did get paid for the hours worked and the correct allocation is made to Canada Customs.
Under the current options to achieve the above, they use Ctrl F6, which produces a Negative cheque. This entry must then be edited to bring it down to a zero balance.