1. There a scene in the first run where Cooper famously says "Diane, I'm holding in my hand a box of chocolate bunnies". I think the only reason the box is on the table is as a link to the past. (Is it past or is it future har har)

You assume that's a bunny ( and Hawk finally settled on it NOT being about the bunny ), it could be a black dog - "the black dog runs at night."

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.

About Hawk's indian heritage, there is a book in Ruth Davenport's bookshelf that has a the title "Indian Heritage". It lies on top of the shelf, to the right. Not sure if this means anything.

I actually saw the bunny as an in joke about over analysing everything and accepting redherrings 😀

The bit about the bunny was to have an excuse for the humor of Lucy eating evidence that was in storage ( though not recently, 25 years ago ).

That's one deep rabbit hole. It's amazing how we find our own symbolism and wish I knew if we are off or not. 

I thought the thing on the card was like an ink-blot version of the owl ring glyph...