For small holes like that, here is what I do;
Blast to bare metal - Both sides.
Brush on POR-15 - Both sides.
Once the first coat is dry, mask the underside of the hood covering all pinholes.
Apply second coat of POR-15 from top only with panel laid flat, the tape will keep the paint from dripping through the holes. Apply additional paint coats as needed.
The paint dries hard, I have covered holes up to 1/8" this way and the rust has not come back.
Barry