Sadly vertex shaders do not update the collision. That said, in some simple cases you can correct for that in your blueprints. For example, we messed with a demo a while back that used vertex shaders to sway an ocean. Part of the sway was a simple single axis sine wave. Because we knew the axis and sine parameters, we could simulate an intersection for any traces to the water plane and have the hit FX spawn at the proper point. That type of solution is not likely to be viable for many cases. In gears3 where we made heavy use of vertex shaders deforming the a level (leviathan smashing ravens nest), we used a series of triggered dynamic blocking volumes to update the level collision.
If you need collision on something that changes shape, maybe you can use a skeletal mesh or a series of them.