It could be for creating a sense of abstraction or to represent something symbolic. Sometimes, such designs are used to evoke certain emotions or to catch the viewer's attention in a different way.
The reason why Wen Zhong had three eyes was because he had cultivated for thousands of years and gradually comprehended the laws of the Heavenly Dao, thus obtaining the power of the Heavenly Eye. According to legend, Wen Zhong was born with a third eye. It had already existed when he was born. His third eye was known as the Eye of Divine Power. It could distinguish between good and evil, and help him become an important official of the Shang Dynasty. Some legends said that Wen Zhong's third eye came from Goddess Nüwa, and humans had a third divine eye to begin with. They could only open it by cultivating the Great Dao. In short, Wen Zhong's third eye was the result of his cultivation and birth. It had a special ability.
One possibility could be a magical experiment gone wrong. Maybe she was trying a new spell that had unforeseen side effects on her appearance, specifically causing her eyes to turn red.
Owl's big eyes are to allow them to see clearly in low light conditions. Their eyes are adapted to gather more light, giving them an advantage when it's dark. Also, big eyes aid in spotting prey from a distance.