As soon as I can install a remote trunk release with my current alarm I am going to disconnect the remote trunk release inside the car for this reason. (And I don't even have anything hiding back there, unless they want my compact spare.) Since you have an SVT you should be able to pop the trunk with the remote, might as well disconnect that lever.
Definitely sounds like someone who knows what was in your car, since everything is gone and cut so clean. Sorry to hear.
