The navigation panel can be resized independently of the main window, so it makes more sense to me that its size should not change upon window resizes. Imagine I set the right size of the panel and then wish to change the size of the main window. I end up having to resize the navigation panel as well. (This happens to me all the time.)

I notice that evince keeps its resizable side pane fixed upon resize of the main window. This makes much more sense to me.