Dave, there is not supposed to be a plug in that hole. Notice another hole in the floor has a plug and a small hole in the center of that plug. It is by design to create an airflow that will pull water out of the spare tire and tool kit area of the trunk. I had the same question and talked to my service advisor at the dealership.I have a 2003 SL500. I noticed there is a ~1" hole in the trunk floor just in front of the spare tire. There is no rubber plug in mine - should there be one??
Dave