Other channels that could become more attractive to advanced terrorist groups could include mobile applications developed for secretive communications and offered through Android app stores. Social media, like Facebook and Twitter, are also logical places where terrorists would go to write coded messages to each other or to hide messages within image files.
"There's so many other alternate channels and it's all embedded in some form of social media," Tran said.
Knowing the NSA's capabilities will likely cause terrorists working in small groups, such as the two brothers accused in the Boston Marathon bombings in April, to "go dark," Steven Weber, director of the Institute of International Studies, at the University of California, Berkeley, said.
"The less sophisticated folks, who are a little bit dumber, quite frankly, they are probably going to go quiet for a period of time," Weber said.
When they restart, they are likely to resort more to communicating person-to-person or by mail, rather than through email or over voice or text on a mobile phone.
"One of the biggest concerns we have today is the lone wolf that operates in a very small circle, either one or two people, and the plans are between the two of them," Herron said. "The smaller the circle, the more difficult it is to intercept."
Sign up for CIO Asia eNewsletters.