Sorry for the late response here. As the person who is both head of technology but also the vfx supervisor, I can tell you Nuke's Stereo SDI output support is poor at best. Nuke handles Stereo compositing very well, however, it is the SDI monitor viewing that is under developed.
We tried using Nuke Studio as a potential replacement for Smoke. We found that Nuke Studio does not support Stereo Left & Stereo Right workflows. This is the common workflow and our pipeline follows suit. In order to view Stereo within Nuke Studio, you must use a multi-view EXR or a multi-view Quicktime. Essentially a single file with both views. This proved too difficult within our pipeline so we abandoned it in favor of a Smoke & RV combination. RV handles stereo like a champ. You can output Left/Right over SDI1/SD2. RV has many native Stereo tools. I would recommmend cutting bait and pursuing RV as suggested throughout this thread. Keep in mind you need RV-SDI for output. It is a different license than RV.
FWIW, we have successfully output Dual Link Stereo SDI1/SD2 through both Blackmagic & AJA devices using Smoke & RV-SDI.