1. I found your
coop. It says in the description: "not suitable for large rabbits, large chickens." I think that includes ducks. I would not keep ducks in a run with a ramp that steep. Assuming a duck needs four feed of floor space, you've got room for 1.5 ducks in there--it's 48x20 inches. Conclusion: do not buy that coop. It's cute, but it's designed for guinea pigs and dwarf rabbits.
2. Ducks are noisy.
3. Yes, you can use baking soda to manage the smell. Be careful about it and make sure they aren't eating it. Also, keep the pen clean. A rubber bin is good--hose it out at least twice a week, dry it, and replace the bedding.
4. There's a very effective setup that I doubt you're using: keep the food and water on wire and separated. That keeps your pen much cleaner.
5. How old are your ducklings, what are your outside temperatures, and what temperatures are you keeping them at? We need to know before we tell you when to put them outside.
6. Ducks love bugs. I doubt you'll have much of a fly problem if you keep them clean. I've never noticed ants being particularly attracted to duck poop. As for feed, there are a lot of tricks for keeping it contained so that it doesn't attract things (and I'd be more worried about rats than ants) Don't let it touch the ground. Minimise waste by using high rubber pans for feed and dampening the feed before you feed it. Feed pellets, not crumbles. Don't free-feed, limit their intake so that they're more careful about not tossing it everywhere.