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.

"What's on the table?", is more natural, as Jon said. "There" could be used when you point at something specific. But in that case this would sound more natural: "What's that (there) on the table?"

there is the verb "to do" that "is the signaling of an object in action. that is to say "that on the table" is the specification of the object. "there is on the table" is that the object or objects are on the table. the correct way of saying it is "there is on the table"

What's on the table? sounds more natural.

What's on the table is more natural sounding.