Am I allowed to have the 144 h visa permit in shanghai?

Your itinerary is definitely and undoubtedly eligible for 144 hour visa free transit in Shanghai because of your itinerary:

Europe - Shanghai - Japan

You will print out your flight and cruise tickets and have those printouts with you. Also, you will declare at check-in in Europe that you will travel to Naha, Japan via Shanghai using 144 hour visa free transit. You will present your tickets and after a short time, you will be allowed to board the plane.

Upon your arrival in Shanghai, you will approach 144 hour visa free transit counter where you will fill out a blue form. Again, after a short time, you will get a sticker in your passport and be allowed to exit the airport. This is all free of charge.

The detail where your cruise makes a dock in Hong Kong is not a problem because French citizens don't need any kind of visa to stay in Hong Kong. Your passport is all you need.

To conclude, you are perfectly fine for your cruise and to confirm once again, you really don't need any kind of visa.