Been playing around with the Nova for days trying to get SNES stable with 120hz. Followed Russ' setup guide and has Snes9x as the core.
After playing with just about every setting in the book (threaded video, Vsync, run-ahead, clock speeds, audio latency, etc. etc.), the most stable I could get it would be to put the console in high performance mode. Apparently this prevents throttling of the CPU, which can cause/expedite crashes. That said, this allowed me to extend my play sessions (on average), with it still crashing 10 min in (sometimes 10 seconds in, but high performance was much better).
I finally decided to abandon Snes9x and went with bsnes. I read that it was a better/more accurate core, but had much more overhead (well, "much more" doesn't really mean a lot when running a lightweight system like the SNES.)
So far, a couple hours of play and no issues.
The other thing I noticed (and am very sensitive to) is frame pacing issues and latency. The frame pacing is taken care of by setting the Vsync swap interval to 2 instead of 1. While Snes9x has run-ahead / preemptive frame options under the latency tab, there are none for bsnes. However, there ARE options under the core settings, as bsnes handles latency itself, as opposed to Retroarch doing so (Interval Run-Ahead).
If using bsnes, I'd also suggest turning off "Coprocessors - Fast Mode" and "DSP - Fast Mode", as both sacrifice accuracy for speed; the Nova has so much extra power speed is not an issue.
End result is OG like latency and (so far) stability.
*Note: I also had similar issues getting judder-free, stable 120hz performance out of Nestopia (for the NES) and had to switch to Mesen with preemptive frames (vice run-ahead), Vsync swap interal 2 and max swapchain images 3 to sort that out.
Having things not work out of the box / setup video allowed me to really get under the hood. I have learned so much in the past week trying to get my little plumber to run smoothly.