I use a combination system. Sometimes the Runners tell me when they are going in, sometimes I tell them.
We have a fairly spacious night pen in our walkout basement because here, the winters can get brutally cold and the snow gets deep and I love not having to shovel snow to get to them, and I love not having to worry about if they are warm enough.
I know it cannot work for everyone - the point I was trying to make before I got off track a little is, that if the shelter is well ventilated, the bedding decent, and especially if there is a setup with food and water that keeps it from getting icky (it can be done), then having them in for more than eight hours is no big problem.
This winter the ducks were in for sometimes 23 hours a day, some days. But they have over 100 square feet for the thirteen of them.
So, I suppose what I need to ask is, how many ducks, which breed, how large is their shelter, can they have food with water in there?
If they want to go in, I would let them in. I also don't let my ducks out real early, as they sometimes are not done laying till after 9 a.m. But days that I must must must get out of here earlier, I let them out and get them settled in and expect to find an egg or two in the day pen.