I've seen CM's make kids take shoes off to be measured before - usually it's the tall platform style flip-flops. If they are like sneakers with a slightly thicker sole, it probably won't draw attention. But if the shoes are obviously adding a significant amount of height, they may get measured barefoot instead, which makes it even less likely that they'll pass than if they were wearing regular shoes.
Other good strategies are to go first thing in the morning, before their bodies have had time to shrink (as they do throughout the day) and make sure to practice standing up tall under a stick. A lot of kids by instinct tend to hunch down when they feel like something is over their head.