'What ails you?' is a very archaic way of saying 'What's wrong?' or 'What's the matter?'. Forget about it. Nobody has asked this question in this way for several hundred years. You will never hear this.

It's not a common phrase, but we all understand it as slightly archaic. You hardly ever see it as a question; it's usually found as part of a (poetic) phrase: "...to cure what ails you" "...good for what ails you" I would not even change the phrase. Use it as a set phrase only, with "you" in the general sense.

as per previous answers, I doubt very much that you'll ever hear this sentence used. In Australia, we might ask this question by saying - 'feeling a bit crook are you?'

It means 'what is wrong ?' or 'what is the matter ?' [UK English] : do you feel sick, or do you have a problem ? It is 'old' English, dating from Elizabethan times, the time of Shakespeare.