Low exposure noise is photon noise, cannot be avoided. Long exposure noise (with enough exposure) is sensor noise, depending on the particular sensor. With extremely long exposures it can be really bad but with "normal" ones, it is less problematic than photon noise.
Subtracting a black frame (LENR) can cancel repeatable noise but it will increase the random noise. You lose even more DR, which is not great with Canon to begin with, and is really needed with night images.
In short, shoot at ISO 100 with LENR off.