Just for the records: I think in my native language I'd use different word orders for the three cases:
Asking whether or not he said it:
Hat Paul gesagt, warum er nicht kommen kann?
(It would normally be understood that I want to know the reason, too, if the answer is positive.)
Asking for the reason why the information was given:
Warum hat Paul gesagt, dass er nicht kommen kann/könne?
(A situation to ask this might be that Paul actually did come in the end, and I wanted to know why he had said he would not.)
Asking for the reason why he isn't going to come (beware, I'm not sure about punctuation here):
Warum(,) hat Paul gesagt(,) kann er nicht kommen?