2013 Model S, no air suspension...rattle started several months ago (at 120K miles) only after the Service Center replaced rear motor drive unit and battery contacts, as well as recall for front steering bolt replacement. It only occurs when going ~10 to 20 mph over small bumpy/washboard roads, not when going over speed bumps at nominal speeds or etc. Sounds like medium frequency metal rattle like loose suspension component joints or as one other member said 'a metal bolt sitting in a chassis hole loose'. I've taken it to the Rocklin Service Center twice only to have rear motor drive unit replaced but that isn't it..and BTW the loaner did not produce that same noise over the same washboard test road we drove so I know I'm not hearing things. Don't want to leave car with them again for several days (they may be good at the Tesla tech components of the car but maybe need some old fashioned regular mechanics for things like this?) so planning to take it to a regular suspension shop and get it up on the rack to see if they can find something loose. Otherwise at 128K now the car is still awesome and holding at 91% of original battery capacity.
Try replacing the front sway bar links. I have 138k on my 2013 s85 and that was the solution to my rattles. You can do this your self if you are out of Warranty.