They do from what I can recall. In DVC rooms, I know this to be 100% true, but I am not absolutely sure DVC villas and resort rooms have the same type of clock radios. If it is an iHome with a 30-pin dock for Apple devices, there should be a small Mini Stereo cord around the back or on the side. It is very short, but it should work.
Edit: Did some checking, can't say 100%. Some rooms have the new iHome radios, some don't. It depends. You could check with the hotel front desk by calling. When you call the number given for AKL, however, you may first be transferred to a call center or another resort that has an available operator, not necessarily AKL. Make sure you are speaking with AKL Cast, and ask away! They should be able to help you.