It's almost the same.
The first assumes you work with standard ipad resolution in the editor (I assume 728 was a typo and it should say 768), the second assumes you work in retina resolution. Obviously, few people work in retina resolution as the desktop monitors generally don't support that yet.
There's also this little hitch - NGUI doesn't really work with half-pixels for widget placement. This means that if you set your height to 768 virtual pixels, then your widgets will not be placed at offsets from that - it means that the screen is divided into 768 units on height and placed on that "grid". Certain things moves widgets off of the grid like Tweens, but for raw placement it falls back to the grid.
This means that with HD, your UI will still only be placed with a fidelity of 768 virtual pixels.
If you go route 1, and set height to 1536, you will have double the resolution to place your UI, BUT on lower resolution, widgets can be placed on 0.5 pixel offsets compared to the screen, making things look a little fuzzy.
It's a trade off. I tend to go with defaulting to low resolution for placement, because it's so much easier to work with, and switching to HD data inside the widgets/atlases while using the "SD" placement.