While this may not be what you were hoping to hear, the answer is: it really all depends on the context. That said, I think this word "context" gets used very broadly in situations like this - the reality is that some of that "context" is word knowledge and common sense. Let's look at some of your examples:
暇ですか？ is almost certainly about someone else, because you know whether or not you are free - in essence that's a decision you make. It would be bizarre to ask someone else.
頭がいいですか is again overwhelmingly more likely to refer to someone else. The reason here is a little more difficult to pin down, but I would say it boils down to the fact that it's very weird to ask someone else to determine ground truths about your own intelligence. Even in English, Am I smart? strikes me as a bizarre question. Note that if it were intended to be rhetorical, Japanese has other mechanisms used to make that explicit like かな.
Now, conversely, if you ask 頭がいいと思いますか？ this could easily be a question about whether the other person thinks you are smart. It could of course also be a question about whether the other person thinks they are smart; this is one of those cases where context really will make the decision. In a vacuum though, I would assume this meant Do you think I'm smart?.
There are always ways to make things ambiguous, though. If you are in a group of three and someone asks 暇ですか?, it would be perfectly appropriate for you to clarify who they were asking about with something like 私ですか or 私がですか？.
Also while you likely wouldn't use the word 暇 in this case, it is conceivable that you could be asking someone else about whether you were free in a sentence like
日曜日は空いてますか？
If that person managed your calendar, and you were talking about your calendar.
