Both are correct. 'what have you been doing' is the one that implies a continuing sense of the action. "I've been studying English, I've been training to run a marathon." "what have you done" implies you want to know what actions they have already achieved. "I ran a marathon, I wrote a book" etc. But to be honest, they could be interpreted either way by the person you are asking. Yes, you can say 'is it implying?' but 'does it/this imply' might be better.