From my limited understanding of flat feet, some people are born with them. As long as the foot is strong, a flat foot doesn't seem problematic. I recall reading about an Army study of trainees with flat feet that found they had fewer injuries.
If your son moves well then I wouldn't worry about the flat feet. Just make sure the shoes fit and that the shoes don't have high arches that cause foot pain. Some children will develop normal arches as they grow.
I'd have your son do some footwork drills, preferably on grass, with bare feet to make sure that his feet are strong.