your trunk vibrations are not being caused by the air passing through the rear deck. In a sense its caused by panel flex. You need to deaden your panels (trunk lid, floor, quarter panels, rear deck etc.) That is what Dynamat and the other companies do, they take the tin-like flex out of the pannels its applied to.
Don't block your vents, your heater and a/c are going to struggle when your windows are up. And you'll be trapped in your own farts because there's no where for them to excape the car.