I just had my hood painted about two months ago. What is involved if i want to put hood pins on there. Can i just drill in the holes or does it have to be reprimed & painted afterwards? I dont want to do it if it will ruin the hood.

Drill the holes. Use a paint brush and paint the raw metal. HTH.

So i just paint the bare metal with a paint brush. can i just use primer or will there be surface exposed outside the pins that will have to match the color of the hood which is blue?

You won't see this area after the pins are installed. But you will want to seal the metal, use primer if you want but do use paint. Primer isn't a good sealer.