Good JWT libraries essentially have a "box" and "unbox" function; the work required by the client needed to go behind the library's back here is on the same level as that needed to behind crypto_box's. Further, crypto_box works on a lower level than JWT encode/decode functions typically do, and would leave many concerns that JWTs handle in the user's hands for them to handle, alone. Having the user write their own code to handle those concerns is a terrible idea.
I'm with you on this. I've never thought of JWTs as a session storage mechanism; rather, I've always thought of them as a simpler (JSON-based) alternative to technologies like X.509 attribute certificates and SAML assertions. If you're creating a ticket / verifiable claim, there are a bunch of security considerations that JWT at least lays the groundwork for, and that NaCl secretbox doesn't appear to offer. Curious what OP thinks about putting things like payload canonicalization, subject/issuer/audience specification, and expiration entirely in the user's hands. I suppose its up to implementors to do appropriate validation, but at least JWT simplifies the conversation a bit.
