As far as I know, flake.nix is hardcoded, so you’re going to use a separate directory for every script anyway. And then there’s flake.lock, which you have to go out of your way to avoid creating, and you’ll be spammed with obnoxious warnings if you still do.

So would you want to fit everything into just flake.nix? I don’t see why. Could you? Yeah, sure: http://ix.io/4ll5 for a single shell script, for example.