Using unformal nicknames is better, or short brother down to bro, and sister to sis, etc. cousins to cuz.
The problem, from the point of view of the author, is that it's not necessarily natural to shorten "sister" and "brother" in their native language. But I totally agree that, while my children often use "sister" and "brother" while talking together, it's when they are either playful or angry. When they are just talking "naturally", they use their name or nickname.
You normally wouldn't address your parents by their first names, neither aunts and uncles.
Here I think that it's a cultural thing, and that it also depend of the relationship you've with them. I never called my parents by their name, but never used something else that their name when addressing my aunt and uncles ; and my cousins do the same. But we are a family that share deep bounds together, often staying to each others houses during our youth, what probably make this more natural than for people who only see their relatives once in a while.
In the same time, one of my uncle always called his father by his name, while the rest of the family used "father" or "dad" depending of the context ; and he never did it with his mother. He loved him, but there always were some tension between them, what probably lead to this choice from my uncle ; some kind of "like I strongly disagree with your views, I'll clearly mark that I don't see you as a fatherhood figure".
This being said, at first I thought that using the full word could be a good idea time to time, because games being generally released by updates, it would be a good reminder that you don't call him "bro" because he's your best friend. But in fact there's enough situations where the full word will be used naturally ; anytime someone talk to the MC about one of his siblings, using the full word would be more natural than using the nickname.
The worse is that it's not even due to the fact that a patch is needed to have the incestuous content. Even if they were your "landlady" and "roommate", you wouldn't called them like that. In fact you would do it less often that you've occasion to do it with members of your family. While, "Mother, can I help you", can feel natural, "landlady, can I help you" seem ridiculous ; you would more surely use something like "Mrs Whatever, can I help you".
As for the roommates, there's no reason for this word to be used, even by someone else, unless it's a fully formal discussion. Even the landlady would address them by their name, asking you to "tell [girl's name] that the dinner is ready", by example ; this while a mother would more naturally come to "tell your sister that the dinner is ready". As for friends, unless they never encountered her, they'll ask "how [girl's name] is doing" ; while they would ask "how is your sister doing" unless they are also friends with her.
But, as I implied above, all this is partly a cultural thing. In Japan generally you don't use someone's first name unless you're really close to this person by example, while in many European countries you'll talk about "Fred from the accounting" even if you almost never talk to him ; in fact, in those countries you'll be more likely to know the first name of a person than his last name, while in Japan it tend to be the opposite.
And this level of familiarity/formality, tend to also define the way you address your own relatives. If culturally you're extremely formal with unrelated peoples, you'll tend to also be formal with your family.
So, to come back to the subject, yeah it fill weird for us, but perhaps that it's the opposite that would feel weird for the author.