A short between certain bent pins, either on the CPU or on the motherboard, can damage the motherboard and CPU. Depends on which pins touch.
Since you said these are on your motherboard I'm guessing it's an Intel socket. Can you show a picture of how the pins are bent? If they aren't bent badly it's probably fine as long as all pins touch the CPU properly when it's latched in. If they are touching or bent too far, they can short or not contact the CPU properly. Could cause damage...or it may just not work at all. Depends on how the pins are bent.