Early (~3 years ago) NYCMesh used cjdns. I am not 100% sure of the reasons, but I think at the time cjdns had bad performance and was much harder to setup. I personally tried out cjdns recently and was pleasantly surprised with the ease of setup, though I still think hyperborea is having scaling issues and Guifi (the largest mesh) doesn't use it.

There is nothing stopping anyone on NYC Mesh to use cjdns, and some of us do run it for certain services.