Stanley, I think I'd believe the dealer if they said not to worry. They aren't God, but they do work on Accords every day. Since your warranty isn't through them they don't have much reason to lie to you. If you are really sweating it, drive to another Honda/Acura dealer or at least a good import shop. If nothing else, your mechanic should be able to write up a description of the problem and an estimate to repair.
I've never heard the 2K knock sound in the numerous Accords I've been in. I'm just throwing out guesses, but it could be as simple as stale fuel from the car sitting for MANY months on a lot. Have you tried to replicate the 2K knock sound while parked? Rev the engine in neutral and see if you hear the sound. If you don't you may actually be hearing a suspension part rattling while the car is moving.