In those sentences, when you use "there," you are indicating a specific place. When you use "it," you are focused on the thing itself, rather than where it is physically. So, "What's on it?" Whatever "it" is, you want to know *what* in on top of it. "What's on there?" You are focusing on the thing itself and its physical location. (The thing being covered) You are pointing out the physical location of the thing being covered. Hope that helps. :-)