In Japan, the Japanese will only eat meat from happy animals. If the animal in question is not happy, the Japanese will not eat it.
In addition, it is very normal to use the whole animal for cooking. If you take for example a fish it is normal that all parts close to what is in the intestines are used in Japanese cuisine.
The different parts of a fish are cooked in different ways. You will find that the different parts are part of different dishes.
This is one of the reasons why the Japanese cuisine is so big and varied.
You can read more about Nigiri sushi for beginners where participants get a deeper insight into different fish used for sushi.