I always wonder about that. Often, in the line at the boarding gate several agents will walk around, compare your boarding pass with your passport (and your face), and then draw a squiggle on your boarding pass (sometimes with a coloured felt-tip pen, sometimes with a biro/ballpoint pen).

It seems to me that it would be trivial to squiggle on your boarding pass yourself, and then claim that you've been checked already. I wonder how much security theatre is happening there, too.