The walk from CCI is not any further then Hojo's- its about the same, if not a tiny bit closer. And, you dont have to cross Harbor, which scares me. The shuttle runs every 1/2 hour (on the hour and 30) to the park, and the 15 and 45 from the park. They start running about 30 min before the park opens and the last one is 45 min after the park closes. There is one shuttle in the evening that is missing- the driver takes a dinner break. We've missed it a couple times, usually once or twice each trip, and just make the walk. Its not bad at all. About 10 minutes, even with small tired kids.
You are right about the room rate, you can sometimes get good deals , at Hojo's. It is still not worth it for us. We usually go in the spring, with the kids fly free on Alaska. When booking a package, Hojo's isnt any cheaper. Especially when you factor in the cost to eat breakfast.
We have never had a problem getting a spot for breakfast. We've had to wait a minute or two a couple times, but nothing major. Ususually I look for a spot to sit while dh helps one of the kids get food. Then I get food for me and the other child.