Well... when I've hatched small numbers of eggs in my hovabator, I've had no trouble with leaving them in 12 or more hours. But my recent experience with larger batches has convinced me that I need to be removing ducklings whenever there are three or four hatched, and placing them, as you say, in a "beginning brooder" (I'm calling mine the "recovery brooder").
What happened for me is that about five ducklings spent the night in the incubator, and they fell asleep in a pile on top of four eggs that were zipping. Those ducks were not able to pop the lids on their eggs when they were done--one wasn't even able to finish zipping because of the pressure from ducklings on top. After letting them sit and struggle for another 12-18 hours, I finally had to help those four ducks out of their shells.
Although the humidity had been perfect and the incubator had not been opened AT ALL during the hatch, the ducklings had been trapped for so long in the same location under dry, sleeping ducklings, that they had all become shrink-wrapped and had to be peeled out of their shells.
I am confident the problem was the ducklings sleeping on them, because none of the other 15 ducks hatched had any trouble with hatching, and the four that did were the four in the corner where the ducklings slept all night.
So, I've decided that the possibility of humidity trouble from opening the incubator every few hours to remove hatched ducklings is less than the possibility of stuck ducklings from being slept on.
Some day I hope to upgrade to an incubator that has a solution to this problem--ideally, some sort of mechanism that uses gravity to move ducklings gently down to a separate area right after hatching. But for now, with the hovabator, I think removing ducklings is a good idea.
Oh, and I *have* had ducklings file their little bills on the fan at the top. So far no major injuries, but they remove their little egg tooth pretty quick against the fan, and it gives them a little shock that sends them reeling. I don't like it, and it's another reason imo to remove ducklings sooner rather than later.
