Emmi is Saba's nine-year-old sister, but that doesn't mean that the two girls are friends or anything. At the beginning of Blood Red Road, in fact, Saba is a total jerk to her, constantly trash-talking and excluding her from the fun sibling stuff she gets up to with Lugh.
What's up with that?
Well, first off, Saba has always had Lugh around, which means that she "never had no time fer [Emmi]" (7.226). But there's some heavier stuff going on, too. The girls' mom died soon after giving birth to Emmi, and Saba completely blames her sister for the tragedy. This issue is even more loaded because their father went crazy soon after their mom's death.
Yup—that's some real stuff. Although Emmi is too young to understand the reason behind Saba's constant string of cruelties, she's clearly bummed that one of the three people she knows in the entire world hates her guts. That's a poor success rate. As for Saba, she makes no bones about the fact that she blames Emmi for their family's disastrous state, telling Lugh that "'if it wasn't fer Emmi, Ma 'ud still be alive." Saba "couldn't stand even lookin at her" when she was born (1.70).
After their father's death and Lugh's kidnapping, Saba continually tries to leave Emmi behind, sometimes even wishing that she could "leave her by the side of the track an ferget she ever got born" (2.42). It's not Saba's best look.
But here's the thing: Emmi proves herself to be a brave and resourceful companion: she sneaks around Hopetown's most brutal prison like a legit spy; she steals back Saba's precious heartstone from the fearsome Miz Pinch; she even proves to be a crack shot with the slingshot in combat situations.
Still, it's not until the King kidnaps Emmi that we realize how close she and Saba have become. Throughout the novel, Saba struggles with the knowledge that she might not have mounted such a serious rescue mission if it had been Emmi who was kidnapped instead of Lugh. In this moment, however, she puts her own life at risk to save Emmi, showing us—and her little sis—how much she cares.
In that way, Emmi is kind of a foil for Saba: we get to see how Saba has grown by seeing how her relationship with Emmi changes.
They might not be as close as Tia and Tamara by the end of the novel, but Saba and Emmi have come a long way since we met them. We can only assume that this bond will strengthen even further as their reunited family strikes out a bold new path for themselves in the rest of the series.