There are encryption-like features in Nuxeo, but whether to use them or not is a complex question, whose answer depends on why you actually want to have encryption. Encryption is a technical solution to a security-related question that should be clearly defined: against what do you want to be protected?
If you want to protect the files stored on the server from casual snooping by a server administrator, then you can use our proof-of-concept XORBinaryManager, described on the VCS Configuration page. It's not really using encryption as XOR is a really simple scheme, but on the other hand any person willing to undo the XOR encryption on the server will also be capable of undoing any stronger encryption we could provide, as the encryption keys would be stored and accessible on the server so that Nuxeo can provide decrypted binaries to the users.
