Only certain games require decryption, Nintendo added extra encryption to some games with the release of 9.6 firmware.
CIAngel doesn't do any decryption itself, which means if a game needs decrypted, you have to do it manually through Decrypt9. That specific CIA file is then decrypted, but still requires signature patching to be able to install and run.
The CFW isn't able to ignore the extra encryption, which is why "cryptofixing" (Using Decrypt9 to do a deep decryption) is required for certain games to run.