My guess, and this is only speculation on my part, is that the original shellfish ban was for bi-valves like clams and oysters. This particular type of shellfish grows very well in water polluted with sewage. Oysters can transmit fecal disease and parasites even though they are perfectly fresh.
Of course, the cool thing is that if moved to unpolluted water, they purge themselves of those diseases relatively quickly. Bi-valves are pretty damn good at cleaning polluted water with no harm to themselves. They feed on the algae that thrive on the nutrients found in animal waste.