Some pesticides are safe around birds - the one I'd use is Permethrin. It lasts a few months. You can spray it around. We do have fire ants here in Australia but not where I live so I don't know much about how to get rid of them, I am sorry.
Have you seen any ants aorund your area, or near the ducks? Amiga originally suggested having a look round for ants - maybe go and see if you can find any evidence of them.
This article here says that fire ants are attracted to food sources and water. If the problem here is actually fire ants that may be why they are coming into the pen.
Do you notice anything on the ducklings that might look like stings?
I know we are working with the fire ant hypothesis here but I don't really know if they'd make holes in ducks' feet like that...
But other than sharp surfaces on the ground, am allergic reaction to plants, or the slight possibility of a vitamin problem I can't think of another good explanation.
Maybe a fungal infection that is eating away at the webbing?? That's a guess!! You could try an antifungal spray on their feet.....something like Blue-Kote or Betadine.
And it could be a combination. In the south, sometimes the combination of thorny vines and fungal infections team up to cause trouble for outdoor pets.
I would actually move the ducklings temporarily until I could figure out what is causing the trouble.
Any chance they could live in your bath tub for a few nights while you keep an eye on the problem?? I've used my bathtub as a temporary duck house....you need to put old towels or something non-slippery on the bottom.
Other than that all the other things sound good. Let us know how you go!
Can it be a hereditory defect? Something with the thinning and wearing of the webbing??
Also in the area that their cage is, has there ever been any fertilzers, excessive salts, herbicides or pesticides? Or anything that may cause the soil to be acidic then normal?