Form 16 is a certificate of TDS. If no tax is deducted for an employee, then Form 16 is not applicable for that employee. However, there is no wrong in issuing Part A of Form 16 with zero tax.
To do so, navigate to System Settings > Income Tax > Form 16 Options and clear the selection for the check box adjacent to Suppress Zero Tax.
Once this is done, you can then include the employees with zero tax, in Form 24Q and perform eTDS filing for the last quarter.