100% agree with you on both these points, really. Thinking of my fellow sailors travelling to Xian, I thought the same, why pay for the full board accommodation and then pay further to leave that behind. My thoughts are that these voyages are once in a lifetime. It might be seeing the terracotta warriors was so culturally significant it was worth paying the extra amount to leave the cruise behind and tour the area while they are there. Since it was a cruise line excursion, they had a guarantee to join the ship. What I'm suggesting here, you would not have that guarantee.
I am really unsure of the data for port cancellations in Japan. Do you know if it is common for Yokohama and Osaka? Are they less likely to happen because these ports are in a sort of bay?
I do feel comfortable saying that in Japan self-exploring is incredibly easy. The trains are beyond anything on this planet for reliability and pricing.(There's not much dynamic pricing as far as I can see, the same ticket tomorrow vs. a few weeks from now is the same.) Taking a weekender—packing lightly, mid-cruise, could be worth it if you know what you want to see.