It's the fact that the experts behind this were able to avoid the surveillance system. They knew exactly what they were doing and knew exactly how the government would try and find them.
The plane has either crashed or is being hidden at a hangar, for example. That's it. I think if it did crash, someone would have found something by now so I'm pretty sure it landed somewhere. This...
A signal can only be picked up at close range to the black box so no..it is not known for sure if the black box has vanished, malfunctioned or been 'destroyed'.