I think the smoke is definitely exacerbating a known trait among many mallard-derived domestic ducks. From about the age of 3 weeks, to about 3 months, their instincts regarding threats are in hyperdrive. Mine went literally overnight from friendly to fearful. Like that.
What you can do is recognize this physiological stage of development and work with it as best you can. From the helpful members of this forum I learned:
Do not surprise them. As you approach, before they can see you, make a gentle reassuring noise. I used to consistently say duck,duck, duck as I approached the brooder. Every time.
Do not corner them if at all possible. Cornering really sent mine. So I set things up so that I could herd them out of the brooder into the hallway for brooder cleanup time. Their first three weeks I worked around them and they were fine. When the fear hormones kicked in, for their own safety I let them out while I worked.
Spend time near them. Take the laptop near them, bring a book, your crochet project, your guitar or flute. Sit - anything towering over them is fearful. I would lie down near them and just chat sometimes.
Approach as low as you can. Yup, I crawled on my belly. I am not proud.
Remember it is a phase, it passes.
My flock is quite friendly. None like to be picked up, but most will come right up to me and stand on my feet, or lean against me. Some like to be hugged.
Treats are a big benefit - thawed frozen peas, lettuce, dandelion, chickweed, kiwi leaves, mealworms, a little dry cat kibble . . . . You can offer this during their heightened fear stage. Just don't expect them to come close to you. Roll the peas toward them. Set the greens a few feet away from you.
Remember they are ducks. They cannot help it, but they can get through it if you can keep it gentle, predictable, and positive for them.
It's done wonders to relax them, and I've also found that they're way more comfortable around me if I'm talking to them.
