I just figured out a workaround that allowed me to e-file the DE-9C in my Accountant's version of QuickBooks Desktop despite having one or more employees without social security numbers.  Before I go any further, it should be noted that this method requires that you have the employee's ITIN.

What you need to do is enter the employee's ITIN in the "Payroll Setup" screen under the "Employees" tab at the top of the screen.  If you try inputting the ITIN directly in the employee's information section in the "Payroll Center", QuickBooks will not allow you to save the information because the ITIN is not a valid social security number but entering the ITIN in the "Payroll Setup" screen bypasses this error.  Then, when you run the DE-9C, it populates the social security number field with the ITIN that was entered and it allows you to then e-file the form.  Just make sure you go back and change the social security number back to all zeros before processing your W-2's at the end of the year because QuickBooks will likely prevent you from e-filing the W-2's if the employee has an ITIN in their information section.

I hope this helps, good luck everyone!