The first question is not grammatical. Had is not generally used to form a question like this; when it's used at the beginning of a sentence, it's usually to start a past conditional, e.g.
Had I known it was going to rain, I would have brought an umbrella.
The correct way to express that sentence is:
Was this painting created by Leonardo da Vinci?
Your second sentence is proper.
The difference between the two of them is that the first one asks about an actual occurrence -- either da Vinci created the painting or he didn't. Using Could have been in the second sentence makes it ask about a possibility, not an actuality. So if you don't know who painted it, but it looks like other da Vinci paintings, you might suppose that he could have painted it.