While scientist can't read "real thoughts" instead of audio signal, spies would be taught to think in a secret language, preferably each spy in a different one, and only translate it, when they need to speak with someone.
Maybe that's how Babel Tower happened :)
I also wonder, if "real thoughts" are universally identifiable between people. I guess not, so reading them will require calibration of thought-reader. So it (the reader) could be tricked by interrogated person, by thinking about different things/ideas in calibration phase, than interrogators want you to think about.
This allows for full blown fantasy style mind wars. Scary, but also cool.