I also have an occasional rear deck thump. It appears over solid bumps. In Canada there is a TSB for the rear suspension. The tech has ordered a vibration, isolation and sound kit for my car. (I don't know what that means, maybe rubber bushings.

Sound can take weird path when transmitting through the car and to your ears. This can be deceptive. Possibly it's the rear suspension and not the deck. When I think of the times, I hear my rear deck thump, it does occur when the suspesion is rebounding, maybe the dampening is off that's why the TSB was released. I spoke to Toyota Canada yesterday and they weren't forthcoming. The person I spoke to was unable to explain exactly what the kit was.