The standard filler panels (778646-01) improve the cooling performance of the system and are recommended whenever there are empty slots.
The EMC filler panels (778700-01) contain additional gaskets to control EMC emissions from the chassis. If you are more concerned with temperature regulation than shielding, consider purchasing the standard filler panels and PXI Slot Blockers
While filler panels are helpful for extra shielding and physical protection, they are not required otherwise.
You can find the filler panels in the accessories section of the PXI chassis product pages. For example, the product page of the PXIe-1085 shows the following among the available accessories: