Yes, they are the same. "You having fun yet?" = "Are you having fun yet?" The second one doesn't sound as natural to me, but is perfectly correct. I think it would fit in a specific situation. A very common humorous expression is "Are WE having fun yet?" Someone might say this to someone else if they are doing something boring / uneventful. He has to ask if they are having fun because he can't see any fun in the current situation.

i'm always having fun~

Understandable!!! 1. Havn't you any fun yet? 2. Have you stared having fun? 3. Are they the same? In oral conversation, changing the statement to a question, "They're the same", you need to raise your voice. But, in writting I wasn't able to notice that "the same" has been raised. So, it is a statement. My answer to your question, they are not the same.

they are the same