What is the difference between 没有 vs 了没有in sentence?
你吃饭没有?
  
  你吃饭了没有?


You are correct! Both are natural and mean the same thing. 

You could also say 你吃饭没?, 吃饭没？， 吃饭了没？, 吃完饭没？，... Those colloquial sentences are used in daily life.