I have some lisp knowledge, so the scheme version doesn’t look frightening to me, but I guess for sysadmins, who should write these kind of files frequently systemd’s TOML like language is much more easier to understand.

People who only know C-style languages tend to struggle with anything that deviates from that too (which is a lot of developers). The Shepard example looks readable to me, but then I’m a Emacs user and have learned a few languages with “weird” syntax so something that looks a bit different is fine.

Why this kind of files should be written in a programming language at all? I guess it’s a remnant from the old times, but I like when tools abstract away the programming parts, and users shouldn’t have to deal with that

It’s user base is akin to the NixOS audience. It’s more aimed at advanced users and sysadmins (with some programming ability) that want to configure their whole system declaratively. Using a real programming language gives a lot of power and flexibility to achieve this that you’d effectively have to create a new language to replicate that (I.e. Nix or Guile).

On the other hand, something like Shepard is potentially overkill for even Nix and Guix. Nix works quite well as a layer on top of systemd to declare a NixOS system, and still gives you enough power to do most things.