The uninstall command removes script files inside .git/hooks.

$ hooked uninstall --help
Remove installed hooks

Usage: hooked uninstall [OPTIONS]

      --all              Remove hooks not installed by Hooked
  -c, --config <CONFIG>  Path to a Hooked configuration [default: Hooked.toml]
  -h, --help             Print help information
  -V, --version          Print version information

By default Hooked will only remove scripts that have a # Installed by Hooked. line in them, using --all however will remove all script files.