I don't want to sound like a total bummer here, but if due to the sneezing and breathing issues you're starting to suspect a respiratory disease, which in ducks would most likely be mycoplasma gallisepticum, I would cull these babies. Reason being I know you have other ducks, and if you somehow transmit such a disease from these ducklings to your healthy ones (and transmitting it is easy to do; you can carry it over to them on your shoes, clothes, feed scoops, feeders, waterers, even the wind could catch it and take it over to the other coops) then you have a huge problem, because once they have the disease, you can never ever ever get rid of it. They have it for life no matter what you treat them with and will pass it to every other bird they come into contact with.
What's worse is that it even can pass through the egg to the chicks, so for example a carrier hen lays an egg, you hatch that, and the baby is already a carrier.
What's worse is that it even can pass through the egg to the chicks, so for example a carrier hen lays an egg, you hatch that, and the baby is already a carrier.