I was sitting on a lake once with a Beaver on floats, waiting for the weather to clear. The ceiling was maybe a hundred feet, and a couple hundred yards viz. All of a sudden, I heard a bunch of geese honking, then you could hear wingbeats, followed by splashing out on the water. The fog cleared in an hour or so, and there were about twenty Canada geese swimming around just down the shore.
I've caught up to a flock of geese on top of a cloud layer with an Otter. (Took awhile
) So I'd say yes, some birds fly in cloud.