I believe it’s due to the whole folder being copied to the store.

Yep. There’s work ongoing to alleviate this but for now it’s a fundamental problem with flakes.

but I need flakes specifically because they allow to have runtime libraries, which shell doesn’t seem to support. (Translating flake.nix to a shell.nix exactly has different execution results.)

I don’t understand. There’s nothing you can do with nix develop that you can’t do with nix-shell. What do you mean “allow to have runtime libraries”? That’s just buildInputs, which is the same regardless of flakes.