"It's not about the bunny! ... is it about the bunny?" Cooper shows a card with a freaky bunny in part two. Hawk then has to find something that is missing, linking to his heritage.
There's a bunny missing. Could that link to Manabozho - the native American trickster god, also known as 'big rabbit'?
I think the missing bunny does represent Dale himself. Mainly because there were several bunnies that looked alike. Andy even offers to get another bunny for Lucy, showing how common they are. I think this could be metatext concerning the several different copies of Dale Cooper that are in play and that one is, in fact, missing. It should also be noted that the bunny wasn't missing while Dale was around. Another angle could be that bunnies have always been regarded as symbols of fertility because of their tendency to rapidly reproduce. That could be seen to parallel the multiple Dale situation. We could also go further down the rabbit hole and analyze the chocolate as likely being both bitter and sweet, which could typify the opposite nature of Dale and his doppelganger.