Is it possible to automatically create a list of links correlated to files on Owncloud folder?

It would save a lot of work, since I would like to add the links into a database. I might even be able to write something myself if there was a .NET API, but it sounds like there is not.

Not exactly sure, what you want to do. You must share files first, before you can link them. For the user himself, you can directly access via webdav.