I'm afraid the Add Service Reference working on OData V3 (WCF data service) doesn't support automatically generating service operations in .NET client. However, you can write your own methods in generated service context class to invoke the operations. Like this:
IEnumerable<Customer> GetActiveCustomers()
{
Uri requestUri = new Uri(this.BaseUri.OriginalString.Trim('/') + "/GetActiveCustomers");
return this.Execute<Customer>(requestUri);
}
With this you can write var actCusts = context.GetActiveCustomers();
and get the results back in your .NET application.