I'm having the same issue trying to list files using the Python API. I've generated a JSON key, set my scopes, and tried to list files.

The service account can list files that were created by the service account. It can list files I created with my personal company account and shared with it. It can't list files that are in a shared folder that is shared with it.

There is a shared folder used by many members of the company that has a large number of folders in it. I need to use the API to list these folders and extract ID numbers from them. The service account has been given access to the shared folder, and appears as a "content manager" in the shared users on the folder, subfolders, and files in each subfolder. It should be able to find these files. If I try to get() one of the files by its fileId that's shared with the service account, it returns a file not found error. How do I make these files visible to the service account?