If it has an integrated headset then it will probably come with the Niner headset. It will come with a seatpost clamp. I got a Rip RDO recently and it came with an extra hanger and a seatpost clamp only. It takes an Inset headset, so it did not come with a headset.
The EMD 9 only came with a manual and cable clips. Seat clamp and derailleur hanger (no extra hanger if thats what you were referring to) were already on the frame. I had to buy the headset separately.
That's a good question. I was looking at the Air 9 Carbon before I got my A9RDO and the LBS gave me a choice of how I wanted the frame equipped. EBB or CYA-PF30, BSA, etc... I would imagine that it comes with one setup. I would call and ask the guys at Outside Outfitters. I've been on the phone with them before and they were very nice and helpful.