There is technically no difference between an NRPN and a CC. The difference is that NRPNs have no definition in the MIDI spec. They are there to allow synth vendors to extend the standard spec by adding their own product-specific commands. This means they usually include some additional data after the command byte, whereas CCs generally add only a single byte, or none at all. With each NRPN command requiring 2 to 3 times as many bits as a CC, I'd be reluctant to use them for continuous automation, although in practice that overhead might not be significant.
So why select one over the other when both options are available? Probably because the NRPN offers more control, such as delay and feedback parameters to a chorus effect rather than just the chorus mix that CC#93 provides. Why
not use them? Because they are instrument/effect-specific, which will make it difficult to substitute another synth or effect in an existing track.