Don't separate .gd scripts from .tscn files in every case, you'll just go mad. I made that mistake on a past project and it was a waste of time and made everything more confusing.
There is a use case for it in parts of the project though.
I'd recommend #2 but with categories, limiting 2 files per folder is overkill, for example you can put all "vehicles" gd/tscn in one folder, etc.
One note is "assets" such as "art" folder will appear first in searches. That can be annoying when you have tons of art with the same name as your code file you're trying to find, because they will appear first and you'll need to scroll down. If you can find another name for it you like, lower in the alphabet, such as "resources" it will help in the long run IMO