As much as it pains me to say it, I think it's likely that a raptor got him. Runners don't typically really "fly," at least not from ground level, though they can flutter and soar for a bit if they start off on a hill. If it were a ground predator like a raccoon or fox, there likely would have been very obvious signs of a struggle inside the pen, and your other ducks probably would have be noticeably unsettled considering the timeframe you mentioned. A raptor can swoop down and grab a small bird almost as quick as you can blink, and they have incredible eyesight to see potential prey from great heights.
You really should consider covering the top of your pen with hardware cloth or chicken wire, especially since it's near a wooded area. You never know what might be hanging around in those trees just waiting to come and scoop up one of your babies. If you let your ducks free range, you should also consider doing everything you can to attract crows because they help keep the raptors at bay. We keep food out for the crows, and we call them if we see raptors in the air regardless how high in the sky the raptors are. Raptors are extremely intelligent, so they do eventually stop coming around so much if you make your environment hostile to their presence.
