They can be time consuming to clean up but replacing all of them is expensive. I've got a small bead blaster and a parts tumbler that work well. Most high end restorers use acid to clean the fasteners. It's fast and effective. I just bought a gallon of muriatic acid but havn't tried it yet. I hear that a 5 minute bath in the acid followed by a 5 minute bath in baking soda water is all it takes for them to look new. EvapoRust is another option but it's expensive($20 for a gallon) and it loses its strength quickly. It does have its place though.
Once the parts are clean, I've had great luck with a black oxide solution I bought from Caswell Plating. It's cheap and lasts a long time. Once the fasteners have been blackened, you can buff them with a shop rag to turn them a med/dark gray. For zinc plated fasteners, you can have them barrel plated at any electro plating shop. A large batch of fasteners only cost me $40. Each shop will have a minimum charge. $40 was the minimum charge at the place I sent my stuff to.
At first I used a penetrating sealer from Caswell Plating but wasn't impressed with it. It works as long as it's applied thick. That changes the look of the fastener and leaves a slightly sticky surface. Lately I've been using RPM( a rust prevention coating) to seal the fasteners. It's invisable and isn't affected when you wrench on it. You can use it on the zinc plated parts but it isn't nessesary. You do need to seal the black oxided fasteners though. Black oxide isn't a "plating" but a controled "rusting" to a black/gray color. Those fasteners will rust quickly if not sealed.