"I don't think anyone really "knows" why this is - I've heard as many explanations as there are people. The simple fact is that this is the tradition we have received from our ancestors and forefathers in the faith.
My own personal explanation for this is that shell fish do not have discernible "blood" and since the blood is linked closely to the soul, a creature without discernible blood is not ensouled and thus can be consumed without unduly inflaming the passions. St Basil the Great also indicates that cold blooded animals (fish in particular) have "inferior souls" because while they have discernible blood, it is "inferior" to that of warm blooded animals. Good science? probably not - but good spirituality? I'd bet on St Basil. By extension then this is why fish is sometimes permitted during a fast but other meat is not. (Being that an inferior soul it inflames the passions to a lesser degree). But then this is all my own opinion and not really necessarily the "real" reason."
Fr. David Moser