What is the difference between 没有 vs 了没有in sentence? Is there any difference the following sentences? They seem the same to me:

你吃饭没有?

vs

你吃饭了没有?
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.