Perhaps that was because they didn't consider them or maybe they did consider them but could not think of any reasons not to use them?
Among the things that S-expressions don't address per se are the interpretation of tokens (e.g., numeric vs non-numeric token syntax), how non-numeric tokens may be interpreted as booleans, symbols, timestamps, etc.; whether to use alists vs. plists for associations and the semantics of any duplicate keys within an associative construct; how to specify the schema for a configuration object (required vs. optional elements & the types of each, etc.)
IOW, merely saying "use S-expressions" over-emphasizes syntax while under-emphasizing semantics.
It's all about config files. Are there people using s-exps in config files?
I’d rather write some TOML/YAML/JSON for simple things where there are a handful of key/value pairs. In more complex cases where you want specific typing, or inheritance, or to solve any of the problems in this article, oh how I wish I could use something like a Guile parser to evaluate s-exprs. It would make life so much simpler.
You could also include anything built on Clojure EDN.
And, in the same way as Elisp for Emacs, Guile is an s-expression based language used not only for configuration but also for extension of GnuCash, GIMP, LilyPond and Pidgin.