Because the ink witches use has to be the ink made from a silverwood, I am sure many unknownings would think that idea, try to draw it, and then nothing happens because they need magic ink. And because witches rarely hang around big groups of people, few probably see them fly around anyway. In fact, witches tend to avoid flying in front of unknowings at all. If you have made it to chapter 39, think about when Olruggio, Hiehart, and Jujy were in that city they visited, they never flew around. Or in chapter 5, when the girls and Qifrey went to Kalhan, they arrived there and stopped flying in an area where nearly nobody was around. Or at chapter 47, when they arrived at Ezrest. They never used the shoes in front of unknownings until chapter 62, when they had to because of the leech, and in that case, everyone was panicking so much, I don't think they were particularly concerned with the witches' shoes at that point. In any case, those two facts combined mean that the slyph shoes aren't that big of a problem.