One way to tell if he is going to be shorter or taller than his parents is measure their canon bones and his........If his is shorter, then he will stay shorter than them, but if his canon bone is longer, he will grow taller. At age two, he has probably reached the majority of his height, but may scoot up a half inch to an inch over the next year or so.
At birth we tend to compare the foal's canon bone to the dam's to give us a general idea of what to expect for height. The canon bone length is what they are born with and doesn't change.