I have heard of this with smaller jewelers, but not with any of the larger companies like Zales. They have camera everywhere and it isn't worth it to them.
I have never had a problem with a ring being switched by a jeweler before. That is an extremely dishonest thing to do; I wouldn't imagine it happens very often.
I have worked in the jewelry industry for over 20 years, and never once heard of this problem. If you think this might happen, map your center stone's flaws.