It doesn't necessarily have to, though : look at plan9. IIRC GUIs respected UNIX's " everything is a file" philosophy, and thus were introspectible, modifiable and scriptable from other programs.

Looking at modern desktop Linux, I wish it had retained more of this. Unfortunately, d-bus, GObject and Wayland aren't really file-based.

It doesn't have to be though, there's just a high correlation between hard-to-automate apps and non-command-line apps. You can e.g. make a GUI app where every button or keybinding is bound to a named function (GUI Emacs comes to mind), and where those named functions can be used in scripts. Another option is to have a scriptable backend; LibreOffice has a terminal interface that lets you e.g. convert between document formats from a shell script, and Astroid Mail is built on Notmuch as its backend which is scriptable.

I think that we just don't have a standard for it. I know people use AutoHotkey to automate a lot of workflows involving GUI applications.

Recently there was a thread about Factorio (the game), which is all about automating. And once you have standard-ish inputs & outputs, you can achieve a lot of automations, in a different way.

It also highlights that the shell has limitations: it's hard to give multiple inputs, and handle outputs and create a complex pipeline. (I guess that's why we have things like Airflow)

That has less to do with being shellable and having a proper library support. The entire Microsoft Office suite is extremely well automatable.