Your points are valid and I was told that there is a special tool that they survey the airframe with looking for just that kind of hidden damage. It will be incumbent on ground crews to fess up when have hit something and the potential for damage exists.
I'm sure that my staement is an over simplificatioin of the process and procesure, but yes, they have made accomodations for this type of hidden damage. I would imagine walk arounds will take on a new degree of carefull inspection looking for any evidence of paint blemeish that may be the indicator of something more serious.