the facts you were given are definitely wrong. Duck eggs ARE safe to eat and even more nutritious than chicken eggs. (See article below).
Duck eggs are recommended by allergists for people who are allergic to chicken eggs as somehow the duck proteins trigger less problems. I personally know several families who keep ducks rather than chickens due to chicken egg allergies in the family.
Any egg handled or stored improperly can cause problems, however it wasn't due to the bloom being left on. The bloom is the protective coating on the egg, applied as the hen lays it, that protects it from spoiling (bacteria entering in through the pores of the shell). ALL eggs have shell pores as the chicks have to "breathe" in the egg (moisture and gasses transport through respiration in shell to remove body toxins).
Eggs that are washed need to be refrigerated immediately as the protective bloom has been washed off. In Europe it is illegal to wash eggs prior to sale as it removes the bloom. Eggs are also stored at room temperature in Europe. (An egg stored at normal room temperature can remain fresh up to 7 weeks on the counter with the bloom in tact.)
Don't use dirty eggs (fecal covered) wherein problems arise. Keep clean nests and collect frequently.
I have never heard of duck eggs being more subject to bacterial problems due to more porous shells. That simply isn't true. Duck eggs have better shelf life as their shells are thicker, not thinner or more porous.
Think about it. The duck hen lays the egg and then sits on them for 28 days to hatch. (A chicken takes only 21 days.) Ducks are in and out of water and around water. They build their nests close to water. The eggs simply have to have sufficient shell and bloom to protect from spoilage or we wouldn't have any wild ducks (or domesticated) in this world.
I've linked some articles below to help with the transition (it does take some tinkering to use duck eggs with baking as they are larger, have less water and more fat content).
So feel free to go get your ducks and eat those duck eggs.
LofMc
http://modernfarmer.com/2015/06/everything-you-need-to-know-about-duck-eggs/
http://www.motherearthnews.com/real-food/the-proscons-of-eating-duck-eggs-vs-chicken-eggs-zbcz1705