Don't think there is any case to use "What it is?" . This sequence happens, but not as a question. What is it? Please tell me what it is.

It depends. As a single-sentence question, you would use: What is it? (Что это? В чём дело? Что такое?) but Nobody knows what it is. (Никто не знает что это) or Does anybody know what it is? (Кто-нибудь знает что это?)

'What is it ?' is the correct form for a question. 'What it is ?' is incorrect and you won't be understood. You use 'what it is' as part of a statement, not a question. For example, "What it is, is a bird and not an animal".

I think, normally it should be "what is it",while if you EMPHASING ，it is "What it is ". Not sure yet. Any enlish native come and tell ？