If you are buried and skirted then it sounds safe. Our set ups sounds very similar, actually. 🙂 I know lots of BYC members let their ducks sleep outside.
If your run is truly secure (what about digging predators, can racoons reach through the bars, do you have weasels?) then that is probably fine. I hear that ducks prefer to sleep outside.
I feel super paranoid about predators, and we live in a predator rich area. We have a predator proof...