We always liked the ones at the far end from the entrance. Or any on the beach side. Check the overhead view of the campground to see where the busy paths are and whether you would rather be close to the shower or close to the beach. If it's windy you might want one of the sites with some protection. The far end used to have a lot less traffic, too.
Answer #2 - The site that is not next to an RV running the AC and watching tv all night.
Full disclosure. The last time I spent a night at the campground was 2 full weeks in the spring of 1980-something iirc and a bunch of us had the last two sites at the far end. When did they start taking reservations? That would pin down the year. The family next door had a generator out in the bushes and ran it until 1 a.m. I was told the next day that their extension cord was stolen during the night. And no, I didn't do it.
I think all four of the NPS campgrounds went to online reservations several years ago, but Ocracoke, being the most popular, had a reservation system long before. From what I remember you can reserve a spot, but not an individual camp site. On the day of your reservation it’s first come, first served.