I agree, the lengths the Nix installer currently goes to really shouldn't be required. However, this particular issue isn't about binaries being deleted. The Nix installer sets up some environment variables for you (in particular includes its binaries in PATH). For a system wide installation, it modifies /etc/zshrc for lack of a better option. Now, macOS likes to restore /etc/zshrc to its default on upgrades, thus breaking the environment variables. IMO this is no-one's fault except macOS.