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I can think of another instance that fits what you're thinking of. Nana Aihara from Kimikiss. She was originally playing the role that Miya played in Amagami, but due to the unorthodox way the game was adapted, she ended up becoming related to a protagonist, but arguably not the protagonist.
As for why this happens, it's pretty clear. It provides a family member for the hero to care about, and, depending on the tastes of the audience (or the audience, regardless) can turn her into a potential love interest. Plus a family having at least one child of each gender covers all the bases.
It's not just little sisters, either. If a character has an older sister, she also tends to fit into certain molds and fill similar roles. They all have their part to play in the story, and when you want to keep your cast small in order to maximize the amount of character time, having characters be related to the leads in some way or another simply makes sense.
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