This is not really a surprising revelation, especially in light of her ascetic lifestyle. I think it is quite normal for people to have doubts about most things in life. Why would a belief in God be any different?
It will be interesting to read all of her correspondence. I have often found (not always) that extremely legalistic and or ascetic people tend to be the most unsure in there belief system. I of course have no way of knowing this about Mother Theresa, but it would not surprise me.
What is remarkable is that she kept going, this shows an inner steel. I also think she will be surprised to now learn that it is during these times of darkness that Christ is holding us up. We just don't realize it. Read the article.