Use security, get a black mark in your file?'s article "As governments invade privacy, tools for encryption grow more popular" mentions a wide spread assumption:

“It’s been co-opted by GCHQ and the NSA that if you’re using Tor, you must be a criminal,” Lewman explained to The Guardian. “I know the NSA and GCHQ want you to believe that Tor users are already suspect, because, you know, god forbid who would want their privacy online, they must be terrorists.”

I wonder if using end-to-end encryption such as PGP and GPG can be a black mark in your file? I've exchanged encrypted email with folks in the government and government contractors. Does this increase my suspiciousness score? Would such activity decrease chances of getting a security clearance in the future?