With incubated eggs, (whether in a 'bator or under a hen) a good deal of the moisture in the egg evaporates. If it didn't the chicks would drown in the shell. The air cell gets bigger, as the moisture evaporates. When the air cell get big enough, the egg will float. In the case of an egg soon to hatch, this means it's good, not that it's rotten.
And no, a momentary dip in water won't drown the chicks. The shells aren't as permeable as that. Just make sure the water's 100F, so you don't chill the eggs, and take them right back out and put back under the hen. (or in the 'bator, as the case may be.) The quick dip in water won't remove the "bloom", either, if you don't rub it. There are people who do this if they can't see the air cells, (very dark shells, or poor eyesight, or maybe other reasons) I remember reading a thread that several people discussed this in, but I don't remember the why. Checking to see if the egg was evaporating enough, I guess.
I wouldn't suggest doing this without know exactly why you would do it, nor would I suggest soaking an egg that's incubating. I can't think of any reason to leave it soaking.
A test for freshness in eating eggs doesn't work as a test for whether an incubated egg is ok. An eating egg that floats isn't always bad, either, just not very fresh. If you break it into a bowl and it looks and smells normal, it's fine.
And I agree, don't shake the eggs!