I think the ship has more to do with trade, as one of the sources of the state's wealth. Philly was one of the nation's major ports and centers of commerce when this seal was created and that ship would be crazy-anachronistic to represent William Penn's.

EDIT: From Wikipedia:

> The Pennsylvania coat of arms features a shield crested by a North American bald eagle, flanked by horses, and adorned with symbols of Pennsylvania's strengths—a ship carrying state commerce to all parts of the world; a clay-red plough, a symbol of Pennsylvania's rich natural resources; and three golden sheaves of wheat, representing fertile fields and Pennsylvania's wealth of human thought and action. An olive branch and cornstalk cross limbs beneath—symbols of peace and prosperity. The state motto, "Virtue, Liberty and Independence", appears festooned below. Atop the coat of arms is a bald eagle, representing Pennsylvania's loyalty to the United States.[2][3]