In his Notebooks, Leonardo does not discuss astrology except for two disparaging comments referenced from the index. In a section collected under the title Prophecies, he says
This brief comment illustrates his disdain for the Nostradamus style of thinking, of speculation ungrounded in observation. A cockerel (rooster) makes noise without meaning.“all the astrologers will be castrated, that is the cockerels.”
This theme is expanded in a longer commentary on painting, available in full at http://people.virginia.edu/~jdk3t/LeonardosParagone.htm:
Leonardo was one of the first and greatest modernists, focussing precisely on what can be seen and describing it exactly. His anatomical drawings are celebrated for this exactitude of description. This contempt for astrology, philosophy and theology as failing to represent nature proved a prescient inspiration for modern enlightened empirical thinking.“As soon as the poet ceases to represent in words what exists in nature, he in fact ceases to resemble the painter; for if the poet, leaving such representation, proceeds to describe the flowery and flattering speech of the figure, which he wishes to make the speaker, he then is an orator and no longer a poet nor a painter. And if he speaks of the heavens he becomes an astrologer, and philosopher; and a theologian, if he discourses of nature or God. But, if he restricts himself to the description of objects, he would enter the lists against the painter, if with words he could satisfy the eye as the painter does.”
So, applied to The Last Supper, these comments indicate that the embedding of the stars of the ecliptic is entirely empirical in intent, that the story of Christ reflects the natural story of the cycle of the year. His secret contempt for the superstition of the church emerges in the placement of the head of Judas in front of the heart of Peter, suggesting that Judas, the grasping thief who denied Christ, was the real inspiration for peter, first legendary pope of the Roman church, the sword-wielding fool who denied Christ but sought to exploit the messiah as the basis of institutional propaganda.