Well, not exactly. Although, Giratina is based on antimatter. There are more than 3 states of matter anyway, you're forgetting plasma. But Dialga and Palkia are based on time and space respectively. I think a better explanation is the one most people go with, that being that pearls are found in water. But another explanation could be based on Ancient Egyptian Mythology, where "space" is seen as a large body of water.