I do not like my students to wear shoes for kicking practice until they have learned proper foot shape, as some shoes affect the flexibility of the ankle and toes. They also keep them from learning to use the muscles in the foot/toes to adjust their balance and grip the floor. I do, however, think that occasional training in shoes is good practice for those same reasons. Afterall they won't have time to take of their shoes when someone attacks them on the street.