Yes, the shoes make a difference - and virtually all schools measure their players' heights with shoes on. At this year's NBA combine - where players are accurately measured to the nearest quarter inch - shoes made an average difference of 1.2". The two most common shoe heights were 1.25" and 1.0".
FWIW, Ryan Boatright's true height without shoes is 5' 10.0", and his average height with shoes is 5' 11.0" - a gain of exactly one inch when measured with his shoes. On the UConn website, his height was exaggerated up to 6' 0".
