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Usually, with a niacin deficiency, you'll notice them having shaky legs, or acting lethargic and not wanting to walk around - if it were a niacin deficiency, I think you would have noticed something off.
You can get Niacin tablets or Brewer's Yeast tablets (I use Brewer's Yeast, because it has other immune-boosting ingredients in it and my ducklings do well on it for the first few weeks, before I switch them to their grower ration) in the vitamin section of any Wal-mart.
I don't think it has anything to do with letting them swim - I let all my ducklings swim at a few days old (in very shallow, warm water) and I've never lost any.
I don't know what could be happening - it could just be some genetic defect.