Or HaChaim on Genesis 3:9/אור החיים על בראשית ג׳:ט׳

1 ויאמר לו איכה? He said to him: "Where are you?" The meaning is: Why do you hide yourself and do not appear before Me? Adam replied that he was afraid because he considered himself naked, and as it is forbidden to stand naked in front of a Torah scroll it certainly is unseemly to appear before G'd in such a state. According to our exegesis, he meant they had become aware of their reduced stature. Their sin had made them aware of the loss of their aura of holiness, hence their nakedness. They could not have referred to actual nudity as the Torah already reported that they sewed together fig-leaves to serve as clothing.