I always make sure that any ducklings I brood know exactly where the food and water I put any shavings in. Ususally I dont use shavings until about 5 days old and I sometimes use some fine grass straw. I always place the food and water in the exact same locations. I find that this helps them to learn the difference between food and shavings. Of course they will still try to nibble on the shavings, but they rarely swallow any. As for the ducklings left outsude with the mother, they are constantly nibbling and testing items on the ground that arent food anyway: so I see shavings as a convenient bedding that is biodegradable rather than using puppy pads or having to frequently wash towels.
Also towels that become damp stay damp whereas when they walk through the deep shavings they kind of turn them over a bit too. Of course they can become very waterlogged around the drinking water, but can be easily scooped out and replaced if you dont need to replace the whole brooder beding.
Hope this had helped to set your mind at ease over using shavings.