Small nitpick, they aren't symlinked to their original position, but instead to a "profile" (global for instance is in /run/current-system/sw, your local profile is $HOME/.nix-profile).
This has several consequences. It means binaries distributed with the expectation of libraries being in their original position (e.g. /usr/lib/libc.so) don't work as is. It also means scripts depending on the presence of /usr/bin/bash are broken (which happen far too often).
I love NixOS, but that is one of the biggest annoyance I have with the system.
With packaged softwares, yeah it rocks and it's seamless.
The problem comes from anything that's not packaged. Things that exist outside the nixos ecosystem.
For instance, the Android SDK is a bit of pain in the neck to install via the nixpkgs : it's a mutable piece of software with pieces that auto-update themselves, made of lots of smaller packages that aren't bundled in the main package, etc...
However, the binaries google provide doesn't run properly on nixos by default because of the non-standard install (has to set LD_PRELOAD so it can find the libc).
Well the Android SDK is like the worst-packaged thing ever :). I thought that its nixpkgs package was one of the greatest efforts to salvage the situation---the XSLT to automatically convert it's xml metadata to nix expressions is super impressive.
This has several consequences. It means binaries distributed with the expectation of libraries being in their original position (e.g. /usr/lib/libc.so) don't work as is. It also means scripts depending on the presence of /usr/bin/bash are broken (which happen far too often).
I love NixOS, but that is one of the biggest annoyance I have with the system.