The Array object has a number of features intended for one-dimensional arrays, because it's a particularly useful case to have a list of items. Push, pop and shuffle are some of the features oriented around that usage, but they can also be applied to 2D and 3D arrays.
If you want to shuffle a 2D array, you should be able to do that by shuffling twice, first on the X axis (shuffling every row), and then on the Y axis (shuffling every column).