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The mod folder is in "documents/paradox interactive/stellaris/mod"
Its not case sensitive.

The .mod file is similar, but you should be able to ask the launcher to generate a .mod for you. Then edit via steam.
I tried to create my own .mod before trying the launcher, and it wasn't detected. May be my fault.
 
I have a related question.
I made a names list mod.
Inside Documents/Paradox Interactive/Stellaris/mod I :
- created a folder : modname/common/names_list/file
- created a mod file with inside
Code:
name="Mod name"
path="mod/modname"
tags={
"Utilities"
}
supported_version="1.0.0"
It shows in the launcher, but not in game.
If I put directly my list into the game's files (in steam/etc.), it works.

Is there something I'm missing, or is the Workshop simply not working ?