For ultimate flavor, you should leave the ham bone in when making ham and bean soup in a slow cooker. By the time the beans are tender, you can easily detach the ham and remove the bone.
Most soup bases are made from stocks or broths that you can purchase from the grocery or make at home. With the exception of vegetable stock, most stocks are made from the boiled bones of the protein of choice. Popular stocks include chicken or beef stock. Cooking ham soup with the bone alleviates the need for a stock and adds to the flavor and consistency of the soup.