I like Himawari's scars because they're something that she chose for herself. She doesn't go out of her way to show them off, but they're still a badge of her determination.

With the other two you mentioned, as well as with Rin in FB, the scars are signs that they were once victimized. The bearer feels compelled to hide them out of shame (or at least Hyakurin does - I'm not very familiar with SDK).