The paint line is the most common method I have seen. I was an inspector and for fasteners in a critical load path we would use an ultrasound machine to measure

The paint line is the most common method I have seen. I was an inspector and for fasteners in a critical load path we would use an ultrasound machine to measure the length of the bolt (these were installed in flange like connections). We would measure them when first installed and compare measurements after that piece of equipment was used. For really critical components we would disassemble them after every use and would perform multiple tests on each piece including fasteners.