It is wise to have the mods under the %appData%\Transport Fever 2\mods\. Do not use the directory mods under the installation directory or you would have to move your stuff after installing an update like the one coming in June.
If a mod is not working or it is not picked up by the game I add a _1 at the end of the directory name of the folder.
It seems that the game needs to have a version number.
Example: you download a mod called 1904456876_no_emissions.zip, when you unzip this file you end up with a folder 1904456876_no_emissions that you would copy to your mods directory. Maybe the game does not like that name, then just add the _1, like: 1904456876_no_emissions_1.
Hope this helps.
Hamoka: suche A 380 Mod für Transport Fever 2
Argelle: Can you even mod the gog version ?!
I have more than 60 mods installed, almost all from Steam workshop, some from transportfever.net, this is the tool I use to grab mods:
https://steamworkshopdownloader.io/
Don't forget to support the modders with some money.