GUIs are tools first and art second.
Any GUI that looks good, but gets in the way, or fails to make the task at hand easy is not a good GUI.
The books and research are about making GUIs functional in an effective way. No one is claiming that a GUI that follows all the principles will look good. However it will make the task at hand easier to perform than it otherwise would be.
The problem is when people in charge of GUIs focus exclusively on Graphic Design instead of UI design. They are different fields, with different goals that only sometimes overlap.