As I mentioned to JD & Sky, I see no reason why you couldn't use the hammocks...
I'm thru-hiking the trail in about two weeks. I'll reserve shelters through the Park's web site in advance for the planned itinerary. If my plans change I will either call the Park office and notify them from the Trail, or just go the Shelter area and take a chance at a site. Since you are sleeping at campsites and not inside the leantos, I'm sure you will have very little problem with assuming a site if plans change.