Great idea that I'll definitely consider using in the future. My ducks were OK when smaller, and I could put them in a cage (rabbit cage). But as they got older, they were even withstanding my push to get them into the cage (for their own protection at night). I only ever got them to walk in...
Depends on how long you plan to keep them or continue raising other birds to replace them as needed.
It sounds like you will let them out in the run instead of free-roaming. So option 1 is out then. Otherwise for free-roaming ducks, they just need a place to go for the night and that option...