They can't be sure. And you have already surmised the reason. Less smaller pitchers make it to the big leagues. Bigger pitchers are just as susceptible to injury as smaller ones. The likelihood of injury has more to do with something we cannot easily and readily measure than height/size, which is muscle tissue and how tight/loose it is near the ligaments involved in pitching (or some crap like that, I always get mind blanks when reading about medical stuff).
But just venturing into the topic, three common areas to look for when trying to determine some type of injury risk would be 1.) how the player "picks up the ball" with his throwing side elbow 2.) position of elbow/shoulder during scapular loading 3.) awkward planting of the foot. And as you could guess, one of the last places to look would be leverage or height.
