I'm sorry you're having to go through this.
I'm going to suggest that perhaps the dog is innocent until proven guilty.
Many moons ago when I still in school, my greyhound caught and killed many of my neighbors chickens.
The neighbor would not manage his flock and keep them out of our fenced yard and farm lots. He turned them out in the morning and let them wander all over his acreage, cross the highways etc.
My dog was inside our fenced yard. He would chase the chickens and catch them. Every single chicken he caught he plucked the rump feathers in mouthfuls and leave them in feather mounds in the yard. THe feathers looked liek they were plucked all at the same time ( no individual feathers). He plucked the feathers hoping the chickens would get back up and run around again. He lived for the chase.
He didn't eat the dead birds. He left them lying where they were. He left the feather piles laying where they were. He never bit/chewed/gnawed on any of the carcasses. Once they stopped "playing" he didn't have any interest.
My neighbor didn't fault my dog for killing his chickens. He knew he should have stopped them from leaving his property. He didn't care about properly containing them on his acreage. I paid him $25 for each one my dog killed because it was the right thing to do. I lost track of how many birds I paid my neighbor for.
I haven't lost a duck to predation but I have seen the remains of aerial predation of songbirds in my yard last winter. There isn't a large pile (mouthful) of feathers in one spot. Predator birds leave behind several individually plucked feathers and blood droplets. Sometimes they leave behind bird carcasses that are missing body parts, internal organs or have grievous bloody wounds on them. (Sorry for the gross descriptions).
If you found nothing at all except some feathers I would guess something caught them and took them back to a den a high perch. I also wouldn't rule out people stealing them.
My current dogs would be all over the scene of the crime smelling the predator scents and tracking it in whichever direction they could follow. Presence of footprints do not necessarily mean your malamute is guilty.
I don't doubt that ducks can trigger prey drive in dogs. My own dogs react in a dangerous way to certain normal ducky behaviors and i know I can never trust them to be alone with my ducks.
I don't mean to bring up hurt feelings. It's hard losing any being that you care for. But I also want to preserve good feelings for your dog because he can't tell you what happened.
Some things are just impossible to know without video recording or observing yourself. I'd hate for you to lose your ducks and also lose a loving relationship with your dog, too.
I wouldn't give up on Dot. She may be hiding in a spot where she feels safe.
Internet hugs and warm fuzzies for you, your flock and your malamute.