They all sound natural to me. I would say they all need question marks, but I'm not 100% sure. Perhaps for rhetorical questions, question marks are not required.
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alc241 What does it matter how old he isYou need a question mark at the end of each. The third stikes me as unidiomatic. I'm not even sure what it's supposed to mean.
2 What does it matter if he comes or not.
3 What does she matter to the company.
4 What do you care if she comes or not.
5 What do you care how old he is.
alc24Can both of these be said?Yes. They can be said.
Who cares who helped you? The most important thing is that someone has.
What do you care who helped you?
CalifJimThey are dismissive of the person you're talking to.I sometimes hear these used in a way which is intended to be dismissive of the third person by way of reassuring the second person.