They do measure in shoes, and the height check does account(somewhat) for shoes. Be prepared to be measured multiple times at the same ride, too. I've gotten DS through at the front only to be measured again before getting DS on the ride. They are pretty hard core about the height restrictions. DS was 48.5 inches last summer without shoes, and they would make him get measured, look really hard at it, etc., and sometimes they'd act like they weren't going to let him on or they were doing us a favor. It was probably the most frustrating part of our last Disney trip because I knew he was tall enough, he was clearly tall enough by their standards, but I guess we got some bored CMs or something who wanted to give us a hard time.
And here's a something about ToT (or at least the one at WDW). The first time we took DS, he was shorter than 40 inches, so we were going to do rider swap. We were allowed in to the queue, only to be told later that he wasn't even allowed to be in the line. The CM ended up taking DS and myself through the CM stairwell to the ride exit. Then the CM gave DS a mini CM outfit that had "Jr. Bellhop" on the nametag. When DH got off the ride, our then 3 yr old DS was standing there saying, "Welcome back!"