The paper deals with the meaning of non-equilibrium temperatures in nanosystems with an internal variable, describing defects inside them, and implications on heat transport. In equilibrium all definitions of temperature lead to the same value, but in nonequilibrium steady states they lead to different values, giving information on different degrees of freedom. We discuss the caloric and entropic non-equilibrium temperatures and the relations among them, in defective nanosystems (crystals with dislocations or porous channels, carbon nanotubes in a solid matrix and so on), crossed by an external energy flux. Here, we present a model for nanocrystals with dislocation defects submitted to an external energy flux. The dislocations may have a strong influence on the effective thermal conductivity, and their own dynamics may be coupled in relevant way to the heat flux dynamics. In the linear case the constitutive relations, the rate equations for the internal variable and the heat flux are worked out and a generalized telegraphic heat equation is derived in the anisotropic and isotropic case, describing the thermal disturbances with finite velocity.