The NFL Combine measures all players without shoes because that is the players true height. The NBA should follow suit to this obvious common sense and do away with the measurement with shoes on. Like you noted in your further explanation that some players differ greatly than others with shoes on it only explains further why this is a completely worthless statistic. I’d rather know the player’s blood pressure or the amount of hairs he has on his pinky knuckle.

Is it possible that some players use some kind of hidden lifts in their shoes to gain extra standing to their height? Why wouldn’t they just go out and find the thickest shoes out there to give them added lift?

If we’re trying to use the reasoning that players don’t ball without shoes then we may as well throw out the measurement altogether and just use standing reach as a player’s height because everybody’s shoulders have different heights. In all honesty who really cares how high the players head reaches but rather how high his hands reach when extending for a block or a rebound.