Shadow clones are disturbed Chakra. The other elemental Clones as well but with an elemental affinity. The Mokuton Bunshin is not just disturbed Chakra, Yamato rather splits his cells and create a clone out of them. Since the Clone consists out of real human cells, it is more capable for fight, cannot be killed with a directly hit (unlike normal Clones) and can stay away much more distant from the original (about kilometers).