His final technique was meant to take his life.
CES cannot be harmful to it's user. Not to mention they are the epicenter of all the destruction that proceeds. So the initial arguement doesn't make much sense especially since you say the manga laughts at physics.
Shockwaves are clearly seen as the ground breaks from where the punch happened outwards, the type of explosion is chakra induced and it just causes the ground to break up more than a diedara type explosion that would bring the same effect if he put a bomb into the ground.
Sakura should be able to protect from sand tsunami with latest feat.
His final technique isn't the only tech that hurt him. I also recall him falling on his own landmines or hovering outside the range of his nanomachines or using hiding like mole to dodge his clone explosion.
A cloud of dust/smoke=/= shockwaves. If her chakra actually caused shockwaves she need not punch anything just releasing her chakra should cause said "shockwave" since as you so kindly put its chakra induced.
Deidara has put bombs in the ground and it hasn't produced the same effect so that's a bad comparison.
Based on the one feat sakura fans love to bring up her punch that "killed all the clones" in fact only killed 1 clone since literally one page later the supposedly dead juubi clones got the jump on her.
The word you want to use its seismic wave. Not shockwave.