Really depends on what definitions are we using. In a strictly biologically sense, no. Roxas is Sora's Nobody, they share the same DNA, so they are twins, or you could count Roxas as Sora's clone. Xion, however was born in a laboratory. I kind of doubt that "Sora's memories of Kairi" holds his or her DNA, so there is no genetic connection there. Thus the answer is no, Roxas and Xion are not related. Also, now Roxas is also in a replica body, so his body's genetics no longer match Sora's, so now there is no biological connection between Sora, Roxas, Ventus, Xion, Kairi, Naminé.
Unless, of course, we DO belive magic overwrites not just appearances, but genetics as well. If we go down that path, and say the whole "your heart will shape your body/vessel" is doing it through literally copypasting your original body's DNA into the new vessel... then Roxas is Ventus's clone/twin, and Xion is more or less Kairi's twin with some Sora thrown in there. Thus, Roxas and Xion are also not related.
That one is easy. The explanation is that she is Ava. Ava somehow ended up in Kairi's heart, and when Sora did his thing in KH 1, she was freed, but not enterily as Ava, more like 99% Ava, 1% Kairi. Kind of like how Vanitas is not exactly that Darkness, but something like that with a little Ventus mixed in. Trust me, I work in Nomura.