This is the first time I've heard of an infestation, Backinwellies! I think duck mites are a slightly different variety but I would treat the same. I would find it difficult to treat the ducks themselves but the house I'd do the same as hens'. Can you catch your ducks and dust them with diatom at least?
If you use chemicals you might have to withdraw eggs, it will probably say on the packet or ask the vet if in doubt!
Good luck, I hope you can get this under control, nasty beasties...