Yup, this is going to come back and bite them. Their "only criminals, security agencies, and banks encrypt everything" attitude means that anyone who encrypts everything they possibly can is a person of interest. As more and more people begin encrypting by default, they're gonna need a bigger net in order to catch all of that data, and the SNR just keeps getting lower and lower.
My old laptop, which crapped out last week, had no trouble keeping up with me, I never found myself waiting for it, and I'm not a gamer, so when I ended up with a new machine that was roughly 20% faster, I decided to enable FileVault on it. I figured, worst case, it'll slow the new laptop back down to what I'm used to. And now, if my laptop is every analyzed by a law enforcement agency, I'll just become another bit of noise the NSA has to filter out.
And Apple has made FileVault a "checked by default" option when setting up a new Mac, so the same class of user who would end up with every toolbar and fake anti-virus in Windows (e.g. average or below average) will have FileVault enabled on their Mac. if Microsoft takes the same route (I haven't installed Windows 8 or newer recently, so I don't know, they may have already), we're looking at something like 2/3 of computer users with file encryption enabled by default, without even knowing it, and some portion of the remaining 1/3 who enabled it purposefully.
I can imagine the high-ranking NSA official who instituted the "record all encrypted data we find" policy, on the basis that only people with something to hide would bother, is sweating right now, as his colleagues are starting to realize he's just made all of their jobs that much more difficult; it has come to pass that only a handful of criminals, and no known terrorists, have made effective use of encryption, but they're still having to sift through all of the metadata recorded along with all of that encrypted data.
Also, before someone else makes the joke: "only criminals, security agencies, and banks" is redundant.