Maybe there's a setting that's got screwed....but I can't see which one would do that.
Have you changed the editor theme?
Editor settings are saved (on my computer at least) in
You can rename that file and launch Godot and see if the files come back. A new
.tres file will be created, so you can quit Godot, delete that and rename the old file back to get your original settings.
If I turn on "show hidden files" in the editor, this is the line that gets saved in the file settings file:
filesystem/file_dialog/show_hidden_files = true
The edit settings file can be edited using a text editor.
Maybe upload your file and I'll try it on mine to see if I get the same thing.