Because of that you can't even just place a chip in there and rip out its innermost secrets. You have to decap it first which is quite expensive or dangerous if you do it yourself since it involves pouring hot acid on the chip that will eat away any organic material it touches.
So yes - a SEM can be used to reverse engineer ICs - just as well as a good optical microscope. But the process is a lot more difficult than "just throw your PS3 into this magic box and you're all set".
If you want to know more on reverse engineering ICs, have a look here: http://www.flylogic.net/blog/
Maybe someone wants to send them a PS3?