That's a good question, the most obvious answer to which is that that is how the card was portrayed in earlier decks like the Marseilles. However, a closer look at the PKT reveals that Waite was unusually talkative about this card, even revealing borderline secret Kabbalistic doctrines:
A.E. Waite said:
17. The Star, Dog-Star, or Sirius, also called fantastically the Star of the Magi. Grouped about it are seven minor luminaries, and beneath it is a naked female figure, with her left knee upon the earth and her right foot upon the water. She is in the act of pouring fluids from two vessels. A bird is perched on a tree near her; for this a butterfly on a rose has been substituted in some later cards. So also the Star has been called that of Hope. This is one of the cards which Court de Gebelin describes as wholly Egyptian-that is to say, in his own reverie.
***
A great, radiant star of eight rays, surrounded by seven lesser stars--also of eight rays. The female figure in the foreground is entirely naked. Her left knee is on the land and her right foot upon the water. She pours Water of Life from two great ewers, irrigating sea and land. Behind her is rising ground and on the right a shrub or tree, whereon a bird alights. The figure expresses eternal youth and beauty. The star is l'étoile flamboyante, which appears in Masonic symbolism, but has been confused therein. That which the figure communicates to the living scene is the substance of the heavens and the elements. It has been said truly that the mottoes of this card are "Waters of Life freely" and "Gifts of the Spirit."
The summary of several tawdry explanations says that it is a card of hope. On other planes it has been certified as immortality and interior light. For the majority of prepared minds, the figure will appear as the type of Truth unveiled, glorious in undying beauty, pouring on the waters of the soul some part and measure of her priceless possession. But she is in reality the Great Mother in the Kabalistic Sephira Binah, which is supernal Understanding, who communicates to the Sephiroth that are below in the measure that they can receive her influx.
The two jugs represent oil and water, or blood, and symbolize her breasts, so it doesn't matter if she's naked or not, her jugs are still jugs.
In the Golden Dawn Tree of Life, I would guess she would represent the limitless space of the universe, inside which we all exist. Opposite her is the male Sun, the giver of life and energy to that universe. So, that's why I would guess she's naked, because we are all, in a sense, "making love" to her. In the Thoth, she represents something similar, but far greater, as her place on the Tree is higher up, and she represents that which is beyond the confines of limitless space. She, too, pours oil and water on the ground and into the stream, only it is probably her jugs are quite a bit larger!
In a divinatory sense, coming after the Tower, she represent hope unseen and unexpected. In way she represents the giving, hopeful side of God, the Shechinah by, um...
suckling the universe...
Waite, however, would probably find my interpretation "tawdry," so go figure. He even goes so far as to take an opportunity to elbow de Gebelin, so it's obvious this card was important to him, with good reason. It's an important card.
