Ideally your layout should be able to cope with whatever aspect ratio the user chooses to use, whether that's landscape, portrait or square. Obviously with an iPad the user can only choose landscape or portrait.
Now how you do this is a matter of choice, but rather than hard code layouts for each mode it would be better to use a fluid layout that "sorts itself out". So in the case of the BBC website it scales the width of images and items to fit and lets the height take care of itself and as there is more content that can fit in the available space this means it has no horizontal scrollbar, but does have a vertical one.
You may have a minimum width for your site/application, but that should usually be less than the width of the iPad in portrait mode (in this case).