Surely they do! Birds fly whether they are inside clouds or not, for clouds are not obstacles for navigation, nor the movement through. ....remember that clouds are only tiny water droplets.You can walk through fog as easily as birds can fly through it,and fog is just a cloud on the ground.
Probably not. It may depend on the species and amount of time in the cloud. So far as I know, the bird has no special organ or ability to determine which way is up -- as opposed to navigation. As a pilot, I can tell you humans definitely do NOT have the ability to fly blind; they must rely on instruments such as an artificial horizon. At least some birds have been observed to tumble out of clouds, whereas others have been encountered in (struck by planes) or above a solid cloud deck. See., e.g., http://elibrary.unm.edu/sora/Auk/v115n03/p0771-p0774.pdf -- doug123w
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