Can anyone advise me what damage this has potentially caused, and if it is reversible? I'm panicking that they may now have issues with their legs permanently, and god knows what else??
Any advice would be greatly appreciated, thanks in advance.
Take a deep breath. It is unlikely you did any irreparable damage by feeding medicated feed. Some people have raised their ducklings on medicated feed and they did just fine.
I think you were on the right track. It sounds like they aren't getting enough niacin. Some ducks are more sensitive to deficiencies than others. You should be adding 1 tablespoon of brewers yeast per cup of feed or about 2-3 cups per 10 pounds of feed. You might want to go with the 3 cups. If it is niacin related you will see an improvement within a week.
Another possibility is they are getting too much protein. From weeks 2-7 you should shot for 16-18% protein. The higher the protein the faster they will grow. This is great if you are raising meat birds for slaughter but its not so good for long term health. You might try reducing the protein to the lower end at 16% to slow their growth a little. But keep in mind that if you feed them treats with lower or higher protein levels it will effect their overall daily intake of protein. If the feed you have is 18% you can cut the protein by adding oats.
To help your little one built some muscle strength I suggest some time in a warm bath. It will allow him to take the weight off his legs and get some exercise. Plus they will have lots of fun.
lomine has written everything I would offer you, as well. Please keep us posted.