If you subscribe it directly from Steam Workshop, the mod gets downloaded automatically to the workshop folder of the game that workshop item pertains to. In the case of Noita, the contents you subscribe to always get sent to your Steam\steamapps\workshop\content\881100 folder.

I'd say installing mods using Steam Workshop is quicker, as it requires just one click and the client will do the rest for you. But in the case of my mods, you also have the option to visit the documentation site that is provided and download yourself the package for manual install if you prefer it that way.