there与on the desk是一个意思,加个there指向性更明确了.there与is并不是there be结构,因为there be结构不与what连用.
There is a pencil on the desk 改成特殊疑问句：
What's on the desk?多谢您的回复啊朋友再打扰一下There is a pencil on the desk 改成特殊疑问句：What's there on the desk? 可否？也可以，不过如果单独做这样的练习时，强调的是what而不是on the desk,所以最好不加there。