ARM Cortex M0 has the provision where user can directly trigger the interrupts without the need for corresponding hardware. For this you can use SetPending() and ClearPending() APIs which basically writes to CYREG_CM0_ISPR and CYREG_CM0_ICPR registers.
Therefore it is better to clear the Clearpending() if somewhere in the project if you are using SetPending(). Else there is no need for calling Clearpending().
Please refer the section 4.2.4 from the Arm Cortex M0 generic user guide for more details.
The interrupts generated by hardware components are sticky and hence you need to Clear the interrupt from component side using Clearinterrupt() API.
Thanks for the explanation Ganesh.