I think every little brood is different. Mine EAT wee-wee pads, and until they were about six weeks old, ATE shavings. We stuck with towels as long as they were in their brooder. Now that they are outside, I use a combo of hardwood shavings and pine pellets. I may switch over more to pine shavings which are less expensive, but to which I am allergic. But outdoors, there is plenty of fresh air and it ought not be a problem. The ducks now just root around in shavings, no longer ingesting them. The used shavings can be composted, creating fertilizer.
The advantage to towels is that the rinse water from cleaning the towels is primo fertilizer water for my garden. Another advantage is that they are reusable.
Also note that some types of shavings produce great volumes of dust - which you breathe, which the ducklings breathe, and in my case, which landed heavily upon everything in the room, requiring major cleanup. If you are brooding them in a shelter outdoors (I can't remember your setup), then the dust is less of a problem, natch.