I think it's very interesting that nothing was ever said about their mother(s).
Being the biological child of his uncle, Yuka-nee is technically his cousin and step-sister, but the way they avoided talking about the mother(s), if we assume that Yuka wasn't just adopted by her uncle (MC's dad) for some reason, leaves open the possibility they could be half-siblings through the mother instead of just step-siblings. When he mentioned his uncle, he didn't say anything about him being dead, which is a critical detail normally present to explain why his cousin was secretly living as his older sister, throughout his entire childhood.
Their situation is just ripe with potential for secret family drama with so little detail given. If it exists, they (successfully) shielded him from knowing. If the truth was something as sordid as them having the same mother, then it's likely his dad didn't find out until Yuka was basically graduating high school, and I guess disowned her after a massive falling out when he learned the truth.
Moving out to live alone after graduating high school isn't so strange, since she'd be ~18 by then, and lots of people leaving for college also typically move out around that time anyway. But what makes it very unusual is that she never visited home again except for that one last time to see the MC, which implies she is not on good terms with her (now step)father. Why would her visiting her old home cause anybody trouble, like she said?
It's very strange for her not to at least visit home from time to time if they were on good terms, even if she was just adopted at a young age. In the adopted scenario, his dad would still be the dad who dutifully raised her, so there's no reason to never show up again after moving out.
This little oneshot is probably hiding a lot more than it shows, but it just suffers from having only 10 pages to work with.