both are used when we speak. but the first one may be more gramatically correct. but like i said, both are used in spoken english and i would definantly use the second one

There is very little difference between these two sentences. I would say the first one implies that a situation is still going on. So let's say I can't read, and I find out my best friend knows. I would probably say "Have you known the whole time?" But, if I cheated on an exam in high school and am now in college, and I find out my father knew I cheated, I would say "Did you know the whole time?". So the first sentence implies an ongoing situation, and the second implies a situation that has already occurred or ended.