He can't do anything to him, but if the child is his daughter maybe he would suddenly ask for some parental rights?
After all this time, he shouldn't dare! Besides, Mitsuki-san mentioned in Chapter 7 that he's got a problematic personality. I doubt that he'd care about Shizuku.
You can never know, some drama is going to be there, or the story wouldn't flow.
Maybe he says something like "you never told me I made you pregnant, I wanted to take responsibility and mate with you, but you just dissapeared, and now I find out that I am a daddy and you took the joy of rising my child away from me".
Just an example, of course it could go any other way.
I suppose that the story could go that route, but given the information we've been given about this guy's personality, (as mentioned in my previous reply) I doubt he'd do something like that. I think he'd try to mess with Naoto in some other way.
Even if the asshat who raped Naoto decided to appear out of the woodwork, Naoto is bonded with Hazuki and is happily engaged to him, with 2 children. I can't wait to see Hazuki beating the crap out of that asshat! (╬￣皿￣)凸 ヽ(`Д´)ﾉ