mike,
I have drilled and used several company's equipment, and the only company that cracked for me (every ball except one) was Ebonite, and I think that is because their coverstock is thinner than most.
I have still yet to have a Track ball crack on me. I have drilled many track balls as well, and have not had one of those crack for a customer either. I think the pro shop may be telling you that so that you will not want him to replace the ball or something.
Depending on the crack, it could certainly get worse. Some people get a crack near the fingers and it never cracks out. The crack itself will determine if it will crack out totally or not.