Wife & I spent the last few days at Emerald Isle, NC. Quite a few of the "tourist" restaurants both on the beach & the Morehead City waterfront have closed for the season, however we found a family owned & operated place that is normally frequented by the locals.
It is called Cox Family Restaurant & is located on US 70, just as you enter Morehead City, across the road from Golden Corral. It is the type place that many folks would not give a 2nd look to. The place is primarily a blue plate special. We had dinner there one night and breakfast there one morning. At dinner, we each had fried seafood plates: I had oysters & scallops; she had shrimp & flounder. The seafood was lightly breaded, not greasy, and more than plenty to eat. A large variety of side items is available, with a leaning toward "country" cooking.
The breakfast was as good as the dinner we had. Typical fare, pancakes, eggs, sausage, bacon.
Prices are extremely reasonable, especially if you are traveling with children or a large group. Way less than the waterfront places - but better food & more of it here, I guess since you're not paying for the water views. This is a cash only business, no checks, check cards, or credit cards. They are open every day except Christmas Day. Well worth a try.