I'm also in this boat. I have atuin as part of my zsh config that is distributed to all new machines, whether they run NixOS or some other operating system with Nix on them (e.g. MacOS). After switching to NixOS I found an interest in maintaining a custom setup again, since it wouldn't fall apart every time I moved machine.

  { pkgs, ... }:
  {

    users.defaultUserShell = pkgs.zsh;

    environment.systemPackages = with pkgs; [
      atuin  # ^R
      eza    # ls
      git
      zsh
    ];

    programs.direnv.enable = true;
    programs.nix-direnv.enable = true;

    programs.zsh = {
      enable = true;
      enableCompletion = true;
      enableBashCompletion = true;
      enableGlobalCompInit = true;

      # https://github.com/zsh-users/zsh-syntax-highlighting/blob/master/docs/highlighters.md
      syntaxHighlighting.enable = true;
      syntaxHighlighting.highlighters = [ "main" "brackets" ];

      # See `man zshoptions` for more details.
      setOptions = [
        # Remove duplicates continuously from command history (preserve newest entry).
        "HIST_IGNORE_DUPS"

        # Instantly share command history between all active shells.
        "SHARE_HISTORY" # Alternative to: "APPEND_HISTORY", "INC_APPEND_HISTORY",

        # Disable ^S and ^Z for less accidental freezing.
        "FLOW_CONTROL"

        # Save timestamp and duration of each command in command history.
        "EXTENDED_HISTORY"
      ];

      shellAliases = {
        # Navigation
        rm = "rm -iv";
        ls = "eza -lg";
        tree = "eza -lgT";

        # git aliases
        # ...
      };

      promptInit = ''
        autoload -U promptinit
        promptinit
        prompt off

        # Simple:
        # PS1='[%n@%m:%~] %(!.#.$) '

        # Colorful:
        # PS1='[%F{green}%n@%m%f:%F{blue}%~%f] %(!.#.$) '

        # Colorful with git branch:
        function git_branch_name() {
          branch=$(git symbolic-ref HEAD --short 2>/dev/null)
          if [ ! -z "$branch" ]; then
            echo -n " [%F{red}$branch%f]"
          fi
        }

        # Omit username, print hostname + '$' with red when root, otherwise green:
        prompt='[%(!.%F{red}.%F{green})%m%f:%F{blue}%~%f]$(git_branch_name) %(!.%F{red}#%f.$) '

        # See: https://zsh.sourceforge.io/Doc/Release/Options.html#Prompting
        setopt prompt_cr
        setopt prompt_sp
        setopt prompt_subst

        export PROMPT_EOL_MARK=""
      '';

  interactiveShellInit = ''
        # Prevent user-level "config missing" message.
        touch $HOME/.zshrc

        # MacOS
        bindkey '^[[7~' beginning-of-line
        bindkey '^[[8~' end-of-line

        # Linux
        bindkey '^[[1;3D' beginning-of-line  # alt+left
        bindkey '^[[1;3C' end-of-line        # alt+right
        bindkey '^[[1;5D' backward-word      # ctrl+left
        bindkey '^[[1;5C' forward-word       # ctrl+right

        # Both
        bindkey '^R' history-incremental-search-backward
        bindkey '^U' kill-whole-line
        bindkey '^Y' yank

        # My SSH endpoints don't recognize modern terminals

        export TERM=xterm-256color

        # ^R only
        eval "$(atuin init zsh --disable-up-arrow)"
      '';
    };
  }