Baking soda won't hurt them, not sure if they ingested Sweet PDZ but its safe to use inside the coops.
When we have a lot of drenching rain I have even used white vinegar around where they like to stand and play in the mud when it get stinky. I pour it into their drinking buckets for cleaning...
Well that's a fur piece from the mountains of NC. lol I have used baking soda over bedding before also. I get the big bags at Sam's club. Might work inside a pen :idunno
Do you mind letting us know where you are? Sounds like you have everything covered as long as nothing can get into your pen. As for smell sweet PDZ works great inside a coop not sure how well in a pen if the pen gets really wet.
Mine will hunker down behind things when it’s windy so you did good with their pen, lots of ideas and you’ll just have to figure what will work best for your area and ducks. Trial and error lol