Sure, keep on using those custom tools
In a galaxy long, long ago an astute analyst realized that "random" is not normal on the Internet. That meant that patterns of "random" traffic were in fact encrypted communications. Since all encryption mechanisms can be fingerprinted, the terrorists (and journalists) using those custom applications are saying "Nah, nah. You can't read this!" while JSOC is smiling and saying "Let me know how that works out for you." as the cruise missile is targeted. PGP is especially fingerprintable.