I'm curious, is there any disadvantage to using Disney's online check-in? It is our first time staying at any Disney resort.
IMHO, no, there's no disadvantage to using online checkin. It saves having to go to the front desk and wait in line, give them your credit card, etc. During online checkin, you enter the approximate time you expect to arrive, and during normal times if your room is ready by then they'll text you the room number and a map, and you can go straight there. Many times we've gotten the room-ready text as we were approaching the resort, but other times we haven't.
Given the hurricane, I wouldn't expect your room to be ready early, but I'd do online checkin anyway. If you haven't gotten the room-ready text by the time you arrive at SSR, you can check your luggage with Bell Services and walk around exploring the resort, swim, go on to Disney Springs, or otherwise enjoy WDW until it comes in.