You need to supply the context!
"What is there on the table?" conveys the sense that there is something on a physical table and you want to know the details.
"What's on the table?" would not typically be referring to a physical table. It would be asking about the conditions of a negotiation. It would mean "what subjects are being discussed in a meeting?" or "what topics are on the agenda?"
But between, for example,
What's in the box?
What is there in the box?
The first is more natural and efficient if you know there is something in the box and want to know what. It would be much less common to use the second, but you might use it rhetorically.