Ah, Collies are usually excellent with livestock.

It's generally the hunting, terrier, and working groups that have problems(minus GSDs, but then, they were originally herding dogs before they were working dogs). Lobo(the white dog in the video/picture) is a Siberian Husky/Akita Inu mix. He's older now, but when he was younger, he once dragged me across the road to go after a cat. I used to struggle with rabbits as well, but now, he's capable of walking politely beside me(he's still /very/ interested in the rabbits and cats, but he's no longer dragging me or pulling on the leash).
I've also heard from other American Akita and Japanese Akita(the type that Lobo is) owners that their dogs know when an animal is family, and when an animal is prey. BUT, I've also heard the opposite, where their Akitas will kill any small animal, even those who were very well-socialized with other animals. So, it really does depend on the dog in some cases.
Anyways, I'm happy your doggy is doing so well with your ducks! Our ducks are just now beginning to come around to the back yard(their run is on the side of the house, but the gate is kept open all day). I'm sure your ducks will see that the dog runs out and will be careful around the door. They're not always the smartest creatures, but they (usually) have self-preserving personalities and quickly learn what is dangerous and what is safe.