Well, who is he, and why does Tomoyo never speak of him?
He is obviously not living with the Daidouji family - but why? Did he and Sonomi break up? Maybe he was violent, an alcoholist or something along those lines, and that's why Tomoyo doesn't want to talk about him?
Does Tomoyo even have a father, in the sense that she knows who he is and has met him? She might be adopted for all we know, or perhaps Sonomi did an insemination (I don't know what Japanese law says about single women doing either)?
As for me, I think that the abscence of a father is a hint that Sonomi really loved Nadeshiko in a romantical way and that she could never find anyone else to love, because Tomoyo doesn't act like she has had a childhood troubled by an abusing parent. I see no reason as to why CLAMP wouldn't throw in a quick scene of Tomoyo's dad somewhere, or mentioning that her parents were divorced, if it weren't for them wanting to hint at something.
What do you people think?