I have a Wind Waker gamepad too. The thumbsticks do seem uneven to the touch, with the left stick seeming to be lower than the right. However if you measure them they exactly are of the same height.
I even woke up today smashing the left side of my gamepad for i guess 6 hours yet the thumbstick's height is fine. It's pretty robust, just like most of Nintendo's products.
So don't worry and enjoy your Wii U :-) Try measuring them so you can free yourself of your worries.