I run zwavejs2mqtt in docker, and my config directory for it is mapped to a persistent folder on the host I can browse to, and have configured to backup to Google drive weekly, so I know mine is backing up. I see the nodes.json and settings.json files on my computer in the zwavejs2mqtt store directory. They are created by zwavejs2mqtt and are not stored in the zstick.
However, since I don’t use the addon version, I preface it with “should” be part of your snapshot. A supervised home assistant install seems to throw files allover the place, so locating them can be difficult, and not everyone of them is backed up.
These files have to be somewhere in the system though, zwavejs2mqtt can’t work without them. If you’re taking a backup of the entire VM you’re capturing everything that way, except the NVM, which is on the zstick. And since the NVM is not as volatile as an ssd, spinning hard disk, or sd card which are constantly being read and written to, I’m not sure you should worry about backing it up too much. But I can understand wanting too of course, but you’ll have to do it manually and periodically
This post gives a directory where zwavejs2mqtt stores files. I would try and find them there.
Also see this note in the documentation for zwavejs2mqtt about backing up
https://zwave-js.github.io/zwavejs2mqtt/#/usage/setup?id=backing-up-settings