Because a spirit is not a goddess. She also seemed to be directly under the Ocean King in the order of things in that world. and I would not consider her a deity of those concepts as an equal to the golden goddesses. Besides we have already seen other lesser gods in similar roles in Wind Waker...
I don't mean to steer the thread too far off topic but does anyone else find it interesting that the bird of the Hylian crest on the shield evolved into a winged humanoid figure? I would love to know exactly what that represents. Might be worthy of a topic itself.
Now on to the topic at hand...