UIAxes behaves like a conventional axes and a uicontainer at the same time for visibility purposes. It has a non-transparent background that cannot be hidden. This is done so that we can support axis off workflows where users still want to see the plots inside of the Axes.
Here is a decent workaround. Create the uiaxes (the one that you want to hide) in a uipanel and hide the panel itself. This requires small changes to your app but will resolve your problem.
Hope this helps.