Diatomaceous Earth, but ONLY food grade, never the type that Lowe's and Home Depot sell. It is a drying agent, kills soft bodied insects as it dessicates their bodies. It is not a miracle product, but I use it in straw in the nests to keep bugs from setting up housekeeping and in feed to be sure any bug that gets in doesn't last long. It helps a bit with smell by drying out whatever it touches. I dust the birds with it on occasion, too. For a pen, I don't think it would do much good, not with ducks, because it gets wet and doesn't work as well. For a smelly pen, I'd say use agricultural lime (not hydrated unless you can keep them out of there till it's rained into the ground or it will burn their feet).
Agricultural lime/pulverized limestone is much cheaper than DE and for a pen situation, I think that would be better and more cost effective. Just till it in or spade it into the dirt in the pen. I think I pay less than $4 for a 40 lb bag of lime. DE will cost you $25-50 for 50#, depending on where you get it.