Is there a way of securing ProxySQL's own SQLite3 database?
I have yet to find a better answer for now other than the SQLite3 DB ProxySQL uses is unencrypted and there are no parameters to change this. It is strange since you can encrypt many other things, but data at rest seems unaddressed.
However one may use HDD encryption to reduce the chances of it being breached. Also, keep user passwords hashed in case your server security is broken, and your encryption keys encrypted.
Will update this answer if I find additional information.