many crates include items for windows which I don’t necessarily need (but there’s no official way to tell cargo that).

The Rust libraries should be marking such code with #[cfg(target_os = "windows")] or similar. And then dependending on what target you compile for, it’ll be included or not. When you compile without specifying a target, then it will target your current OS and therefore not include the Windows-only code, when you compile on Linux or macOS.