I'm having the same problem lately with my LG G5, where the fingerprint scanner just seems to completely quit functioning. I tried to scan another fingerprint into it, and it wasn't picking up anything at all, it just seems to shut down. Restarting the phone usually gets it working again, but sometimes not for long.
I'm also using Nova Launcher, however I've been using it for the last 2.5 years on this phone without any issues. It's just the last month or so that the scanner seems to stop functioning. So I really don't think Nova can be blamed at all. I'm thinking it's more of a hardware issue going bad.