Why is the Web Api returning empty json results with "$ref="?

It's coming from the JSON.NET serializer. It's preserving object references. Take a look at the following blog post. I guess you have some circular references in your object graph and JSON.NET is doing it's best in a desperate effort to serialize this EF structure without crashing (which is what most JSON serializers would do anyway). It's not a standard though.

Personal advice: never serialize your EF entities. Always define view models and have your Web API methods return view models containing only the properties you are interested in.