You would have a pause between the first and second part of the sentence. So I think it's better written "It's true. Or is it?" If someone said this, he/she would be making the statement, but then doubting him/herself right after saying it. Same thing with your second sentence. A person would say "He's handsome. (pause) Or is he?" and then you know that that person is doubting their first thought. This construction can also be used when you want somebody else to questions something. If I say to you "It's true. (Pause) Or is it? (said in a mysterious tone)", I'm indicating you should question what I'm saying.
That might all be confusing, but I hope it helps.