I agree with Chris that English is sufficiently flexible and imprecise that either answer could convey the meaning. It seems silly I know.
The way I would understand it is that an abbreviated query like "No update yet?" has an implied context which we need to fill in, something like:
"(Am I correct in thinking there has been) no update yet?"
Like Animal says, I'd normally try to recognize the uncertainty, and aim to accommodate the context in my reply, rather than just saying yes or no.
Our response is influenced by our understanding of the implied context, and I'd answer much the same as Animal suggests.
However in an informal context like a colleague I speak to about computer matters frequently, I might well simply answer "No", and it would be understood as "Correct, there is no update."