As said by the other commenter, most of these patches are caused by NixOS not using the FHS (except for /usr/bin/env), which can be considered as a good thing in itself. In an ideal world, it would not be a problem (programs should not assume anything about the filesystem hierarchy, and should always use $PATH or their own environment variables).

The issue of integrating with other language ecosystems is indeed very problematic (and it's a very hard problem), especially with regards to the chain of trust (by the way, it's not completely broken, you can still read the original package hash in the derivation, and evaluate this derivation to get the Nix derivation hash), and with regards to the fact that including all of the packages of every ecosystem in `nixpkgs` is not doable.

There is also the (related) problem that evaluating a configuration implies evaluating `nixpkgs` itself, which requires a good amount of available memory, and this can only get worse as `nixpkgs` grows.