"Is it Hannah (on the phone)?" "Yes it is." "Is her name Hannah?"/"Is that Hannah?" "Yes it is." For the answer to be "yes she is," the question would have to be something like "Is she five?"

"Is she Hannah?" "Yes, she is" are both correct. You wouldn't want to say "Is it Hannah?" because "it" is used for objects/things; use "he" or "she" for people. (Edit: see Alisa's answer for an example of when you could say "is it Hannah?") When you say "it's" (the contraction), you want to have something after the word. For example, you could say "Is it yours?" "Yes, it's mine." But if you just say "it's" without anything afterwards, it sounds weird; say "it is" instead. Let me know if you have any further questions!