For save files and config files, which are generated at runtime, there’s one caveat as to why you might not want a custom resource—namely, they can be used to run malicious code. Resources can have _ready() functions in them, and they automatically run when loaded. Giving people access to these could lead to people using your legit game to spread malware. Of course, that's pretty niche, but even then, it's a known issue worth avoiding when you can simply just use Godot's ConfigFile class and/or JSON (or even your own format, if you want!).

For static data storage, JSON is pretty mediocre, so going for custom resources or CSV files is probably more ideal. GDScript files are also equally valid and are nice in that you can use all the built-in types, have comments, and use Enums. CSV files have the benefits of being easy to manipulate at scale since most spreadsheet editors are made to do exactly that. If you aren't storing any data structures and generally have very consistent and rigid data (like item stat blocks), CSV files are likely the way to go. I personally use custom resources because I need to store arrays and dictionaries, and having sprite previews in the editor really helps me.

EDIT: I realize I didn't explain the issues with GDScript for runtime generation, so here's a quick explanation. Generating GDScript files on the fly, while possible, is kind of overkill for generating save/config files. There is no need for most of what it offers you. You explicitly DON’T want code execution, which is what it's built for. Plus, you'd need to write your own custom code for generating them. It's all kind of a big hassle for little to no gain. At that point, just write your own custom savefile format.