AFAIK these returns are sent back to Nikon USA, because once the camera is sold and shipped to a customer, the retailer has no knowledge of what might have happened to it while it was in the possession of the customer.
So they get sent back to Nikon (in this case to Melville, NY) to be thoroughly inspected and tested.
That's the source of the large majority of the "factory refurbs" that you see for sale. I would call and ask someone at Nikon what they think about this.
What are you going to do when the replacement camera arrives and it has 98 shutter releases? To me that would equate to about 4 weddings at my rate of average 2500 per wedding. I've had a "long standing" relationship with this local retailer and the salesperson, so I had no hestitation, especially with the additional discount offer! I've never checked the shutter count and probably won't till it's replaced!
I expect B&H would exchange it (if you don't use it) for another, but where do you decide the "acceptable level" should be?
Every new camera here I have bought has a hundred or two clicks on it too.
Maybe they actually test the things in Nikon quality control; and do not reset the counter?
Maybe somebody at B&H tested it so you got a known good unit?