The important thing is - probability theory doesn't depend on rhetorics. Someone speaking the "nothing to hide" argument, or someone else finding arguments against it convincing, doesn't suddenly invalidate Bayes' theorem! Trying to argue from principle is a mistake because reality doesn't listen to principles. The only relevant question is whether encryption/Tor/whatever is or is not currently an evidence for/against being an evildoer, and how strong that evidence is.
Those considerations do include things like loss of utility because of false positives / false negatives, too. So for instance, it may be so that evildoers are more likely to use encryption than general population, but there's so much normal people using encryption that you can't get evidence for being evil out of just noticing that a person uses encryption (the same considerations explain why so much of what TSA is doing is security theater).