Arriving twice by cruise ship

You did not mention what is your point (place) of departure just before arrival in Shanghai! This is very important detail. In case that you are arriving from some place that is not within mainland China and not Japan, you would be eligible for 144 hours visa free transit. In case that you are arriving from Hong Kong, that would be just fine. So, something like Hong Kong - Shanghai - Japan would be great.

Your way back is just fine because it is Japan - Shanghai - Thailand, so definitely covered by 24 hours visa free transit. There will be no need for 144 hours visa free transit during your second arrival in Shanghai because you will stay there for less than 24 hours.