I am not familiar with "app zapper" aps. Please expand your comment.
That's just one of the complications of the macOS environment. You have to worry about vandalism to your app or its data from users or other developers. There are whole categories of apps that are designed to uninstall, "clean up", or "control" your app. Don't bother suggesting to users that they not use these apps. Users adore them. But until Apple finally goes all-in on iOS for the desktop, you have to live with them.
You don't need to take any action in your app. Just do what you should do. Store app settings in user defaults. If you have more data than is appropriate for user defaults, store it in the appropriate directory such as "Application Support". In the sandbox, there are a few such locations you can use because "Documents" and directories under "Library" are private to the sandbox.
But, if users report problems, you always have to ask about "app zappers", "clean up", "Little Snitch", and antivirus app. Any of these can block, delete, and/or corrupt your app or it's data.
PS: You mentioned "environment variables" above. While these do exist on the Mac, they are typically not useable as such, at least not in the traditional sense. You should expand on what you are attempting to do.
