The reason that JAL use Nikko Narita because inside the hotel, has the check-in counter for both JAL and JAA, you can check-in your luggages over there, so that you don't need to spend the time on the bus, check-in again in the airport.
I have once stayed at the Nikko Narita. The outbound flight from ORD to HKG is fine, but the inbound flight for HKG to ORD requires a night to stay in NRT. If you book through the travel agent, they usually tell you all the information of how to get to the hotel. Outside the immigration, there are a bunch of tourist, hotels pick-up stops, make sure you find the right one, they are mostly written in Japanese. It is a free shuttle, but that shuttle bus is not just for Nikko Narita, I believe it goes to another Nikko hotel too. There are like 6 or 7 restaurants inside, dinner is NOT included, a buffet breakfest in the morning does. When you check-in at the hotel, the front desk would give you a coupon for the breakfest. In the morning, you luggages are usually already waiting for you at the check-in counters (only 2 check-in counters), you should check-in before you go to have breakfest, or you have to wait a long time. This is Not a very recent experience though, however, I talked with my travel agent, JL does not change a whole lot.