I am having this same problem. I have an SGS4 with Nova Prime and the Tesla Unread Count app installed. My stock email icon still has the unread badge, but my Gmail badge disappeared several weeks ago and won't come back no matter what I do. I've checked and rechecked my settings for Nova, Tesla Unread and Gmail, and I've turned the notification off and back on several times in the hope that it would help, but no luck. I even downloaded the new Nova update today, but that didn't help either. Any ideas?
FWIW, I first noticed this problem not after a Nova update, but a Gmail update (the one where they reorganized the inbox into Priority, Social, etc.).