It appears that Mother Teresa's crisis of faith won't affect her chances of achieving sainthood:
Mother Teresa has already been beatified, said Monsignor Robert Sarno, who is in charge of her case at the Congregation for the Causes of Saints. For her canonisation as a saint, she now requires one more verified miracle. Mgr Sarno said it was not surprising that Mother Teresa had, at times, turned away from God.
Apparently she wasn't an agnostic, but a devout believer who didn't find evidence of God in her life.