So if anyone is still wondering, it's meant to represent the blush in the cheeks of the face, due to manga having a large influence and shading could only be obtained from black and white, the lines are meant to be the blush, and it carried over to anime, and now it is not only a stylistic choice, but some artists do it for the same reason, and that is to signify the blush, just like how blush over the nose is drawing with lines.
As a guide, dark-blue is usually when a character is embarrassed or tired, (Sometimes bruises), red means that the character face is blushing either from embarrassment, or due to being angry, and black means its just the tone of the face.
TL;DR: It is drawn to be like the blush on the a persons cheek