It's possible defeating encryption is the responsibility of another top secret department whose work remains unleaked.
Breaking pgp like encryption would require a huge mathematical breakthrough in how prime numbers work and their discovery. It would also require unknown math geniuses to work for said secret department which is unlikely, most of the best mathematical geniuses are already known and tend to work at universities/public research/private research and publish their work there. Not saying this is impossible but it's really…
Likewise with the CIA. From the 1% of the documents leaked so far, there's no evidence that they have the ability to crack modern encryption. But the documents leaked seem to come from a contractor (or were shared with a contractor) so there are likely internal-use-only tools with greater capability than shown in this leak.
That's not to say that they definitely have ways to break modern crypto, just that we can't prove that they don't given the material publicly known so far.