Secret government agencies don't tend to tell you what they can or can't do. So, even if they have hacked into the bad_guys computer and decrypted the messages instructing people to place the bombs you're not going to hear about it.

In the UK we've had some weird private courts (where NOT EVEN THE ACCUSED KNEW WHAT THEY WERE ACCUSED OF (caps because really come on even I think that's bad)) and in the US I guess the intelligence is passed onto to other agencies who then claim the arrests and other evidence is used for convictions.

I know that NSA and GCHQ have very smart, capable, people working for them. I have no doubt that if GCHQ wanted to get access to my hard drive they'd find it trivially easy to do so. Whether those people are allowed to operate at that kind of level (because of oversight or internal politics or they're just doing different work) is another matter.