swap out your heavy subs for 1 8" or 10" and call it a day. no more trunk rattle and you dont annoy everybody you drive past. you will have plenty of bass for sound quality inside the car. also the reduction in attention whoring will cut back your odds of theft.
but if you dont wanna do that, you can put some dynamat under your license plate, thats where a lot of the rattling comes in. also the frame support for your deck lid will vibrate in some spots. you can shim that or use some foam insulation to absorb the vibrations.