Ok, let's think about this for a second:
This atlantis is 3 1/2 miles down correct?
Atlantis was supposedly sunk by an earthquake?
Don't you think, that if an earthquake strong enough to collapse a land mass (island) 3 1/2 miles would totally destroy anything that was remotely a straight line? Just look what happened to that highway in California, it was totally broken up. Now drop those pieces in 3 1/2 miles of water and they'd be spread all over the place.
Now just say for instance, that the city wasn't broken into a billion pieces and that somehow it remained relatively intact and just sunk straight down. Have you ever dropped a beer cap into the water and watched to waft all over the place while it sunk? A ship is pretty hydrodynamic and they rarely fall straight down.....