I’ve unfortunately got no idea.
I’ve only rarely used Netlify Functions, normally we work with Google Cloud Functions.
I believe that’s the case, based on this answer in another thread:
I can’t give you any recommendations on best practice way of working with it, since as mentioned I don’t work with it.
Other threads discussing function organization had suggestions of using any folder structure that you would like, and creating your own build script to move the files to the required Netlify location at build/deploy time.
The main takeaway though is that you can’t use the folder structure to organize your api paths, e.g.
/user/create
/user/delete
/user/update