One can have a shell.nix that uses the flake.nix in a subdir. Here's how one can do this:

in shell.nix:

let
  lock = builtins.fromJSON (builtins.readFile ./nix/flake.lock);
  flake-compat = fetchTarball {
    url = "https://github.com/edolstra/flake-compat/archive/${lock.nodes.flake-compat.locked.rev}.tar.gz";
    sha256 = lock.nodes.flake-compat.locked.narHash;
  };

  src = builtins.path {
    path = ./nix;
    name = "source";
  };
in
(import flake-compat { inherit src; }).shellNix

in ./nix/flake.nix:

{
  inputs = {
    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
    flake-utils.url = "github:numtide/flake-utils";
    flake-compat = {
      url = "github:edolstra/flake-compat";
      flake = false;
    };
  };

  outputs = { self, nixpkgs, flake-utils, flake-compat }:
    flake-utils.lib.eachDefaultSystem (system:
      let
        pkgs = ((import nixpkgs) {
          inherit system;
        }).pkgs;
      in
      devShell = pkgs.mkShell {
        nativeBuildInputs = [ pkgs.hello ];
      };
    )
}

Or whatever your flake is. Mostly important that we have flake-compat.

Then do a nix flake update and ensure the nix/flake.lock file exists. At that point nix-shell (in the repo root) will start working but will use the nix/flake.nix content, and only copy files in nix/ into the store. This does limit to some extent what the flake can do, but for many devShell uses it's sufficient.