If I refinish a hardwood floor that has lots of nail holes in it from subfloor will it look horrible?

Actually, if you have the holes filled and then sand the floor it should come up beautifully. We just had a 118 year old floor done (and we had to replace some wood that was water damaged). The floor had been covered with a cement layer and then italian tiles put over that. We had lots of nail holes too from the cement sections they had nailed down. However once refinished it is absolutely beautiful and with the sanding, you can't tell the old sections from the new sections. Good luck and I am so happy to see there are people out there who appreciate the beauty in the old floors.