The content of DoC doesn't negate the possibility of Vincent being Sephiroth's father. If anything, I personally think an argument could be made for Vincent's uncertainty about the issue within the game (which I'll go into below). It's the ultimania guides explicitly stating that Hojo is Sephiroth's father without even bringing up the question of Vincent's paternity that negates the likelihood of Vincent being Sephiroth's father.
I don't think Vincent thought that Sephiroth was his son at the time of that scene on the cannon. If for no other reason than that Vincent would have known either way that Hojo THOUGHT Hojo was the father, so Hojo stating that he is Sephiroth's father wouldn't be any big revelation to Vincent. Kinda like this:
Vince: "Lol Hojo thinks Seph's his kid but actually I'm the father."
Hojo: "Sephiroth is my son."
Vince: "!!! OMG NO SHE LIIEEDDDD."
Does not make logicness.
I chalk it up to poor translation, I guess?
I think what that scene was supposed to convey was Vincent's surprise that Hojo only ever cared about Sephiroth as a specimen and not as a son, which is a weird place in the dialogue to put that reaction, but I believe we've already covered ad nauseam how poorly that scene was translated in a way that accurately conveys what it was supposed to convey. (I can probably dig up the other threads that go over it if anyone needs me to.)
Either way, nothing that Hojo reveals to Cloud there—in English, at least—is new info to Vincent. (Except
maybe the "It’s my desire as a scientist" bit, if that's meant to contrast the "It's my concern as a father" implication.) So his surprise is weird.
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What I mean about DoC hinting at Vincent possibly having been unsure about his paternity or lack thereof at some point in time is this:
Vincent: Is it true?
Hojo: Is what true?
Vincent: That Lucrecia...that..Dr. Crescent is to take part in this project?
Lucrecia: It’s true. Why are you so surprised?
Vincent: But using your own child...for an experiment?
Hojo: HA! I don't know what you're implying, but both of us are scientists. We know what we are doing. You are the last person to have any word in this. Now, leave us at once, boy!
Vincent: But...
Lucrecia: ...But what?
Vincent: ...
Lucrecia: If you have something to say...say it.
Vincent: Are you...are you sure...this is what you really want?
Lucrecia: Am I sure...? Am I sure?! If this only concerns me, then yes, I am sure!
Vincent: Oh...I...I just...
Narrator Vincent:All I did was watch... I didn’t even try to stop her...and then...
Emphasis on words that were emphasized in speech.
Here's the Japanese version for comparison, but I don't know where this translation comes from or how accurate it is:
Vincent: Is this true?
Hojo: About what?
Vincent: I’ve heard about this project from Lucrecia... [He changed his way of addressing her in the middle of the sentence.] I heard it from Professor Lucrecia...
Lucrecia: It’s true. So what do you want to do about it?
Vincent: Using the child inside your stomach for this experiment...
Hojo: HA! Do you know what you are talking about? She and I are both scientists. Moreover, this is OUR problem. Do you think it is the time for an outsider like you to speak?
Vincent: No...
Lucrecia: What?
Vincent: ...
Lucrecia: If you have something to say...say it right now.
Vincent: Therefore... Are you...are you really going to...
Lucrecia: What do you want to say? [Note: The original is “Nande ‘kimiha’ nanoyo!” I guess she wants to say, why do you have to be so polite and considerate towards me?] Are you talking about me? If it’s my problem, then it has nothing to do with you!
Vincent: Ah...right...even to me...
Narrator Vincent: I just wanted to see it... I wasn’t able to stop her...and then...
So, just considering the English dialogue, for now, we have Vincent approaching Hojo and asking him if something is true. Hojo asks Vincent to clarify exactly which issue Vincent is seeking verity about (implying there could be more than one issue). Lucrecia comes in and challenges Vincent a bit on his personal feelings about her using the baby for an experiment.
Now maybe it's just me, but I see this as being a very masochistic scene for Lucrecia where she's kind of like, she put all the pieces in place to fuck up her love life, like dominoes, and she's looking at Vincent standing in front of those dominoes, and she just needs him to knock them over, but of course he's being timid and polite because he's Vincent. And she's like, "Come on,
do it. Push them over. Ask the questions that will hurt you enough to kill everything so that you and I can't possibly even be an option." And then she's even more angry because he's being so fucking nice and polite about it.
So she goads him a bit, pushing him to push the dominoes. "Why are you so surprised?" Or I guess in the Japanese version, she asks, "What do you want to do about it?" which seems even more direct and confrontational.
Vincent stammers and awkwardly cites his uneasiness as the morality of her actions, in English. In the Japanese translation, I find it interesting that he apparently refers to the baby as "the child inside your stomach" instead of "your own child." Maybe it's a poor translation thing, but "the child inside your stomach" sounds less "this baby issue is obviously a you thing and not a me thing" and is more ambiguous about who the baby might belong to.
That's when Hojo interrupts with the opportunity to mock Vincent. "HA! I don't know what you're
implying, but both of
us are scientists." He stresses both "implying" and "us." "Implying," as in, "There's something else you're trying to get at here," and "us," as in, "Me and Lucrecia and not you." Does that not hint that Hojo might be implying that
Vincent might be implying that the role Hojo plays in deciding what happens to the baby could actually be Vincent's role instead? It sounds to me like Hojo is saying, "Lollll butt out, this is MY kid, not yours." And suggesting that Vincent is implying differently, well, implies that Vincent might have thought differently.
"You are the last person to have any word in this. Now, leave us at once,
boy!" I think him calling Vincent "boy" is odd and I'm not really sure what they were going for. I also realize there doesn't seem to be the same weirdness in the Japanese version, unless Hojo speaks to Vincent in some Japanese verb tense that implies an elder speaking to a child or something. It could just be about the scientist/Turk distinction. Or it could be a way of calling Vincent's masculinity into question because he wasn't the one who knocked up Lucrecia, punctuating his whole point with that.
In the Japanese translation I have, Hojo instead says, "Moreover, this is OUR problem. Do you think it is the time for an outsider like you to speak?" which I think is even more explicit in calling to Vincent's attention his lack of paternity.
Which, of course, isn't about Vincent's necessary lack of paternity, but that Hojo seems to think Vincent might have had a question about it.
Vincent says, "But..." and trails off. Lucrecia sounds like she's gritting her teeth when she asks, "But
what?" And then when he doesn't say anything, "If you have something to say...
say it." Pushing, pushing, pushing his goddamned timid hand toward the dominoes.
"Are you..."
She waits.
"Are you sure..."
She's still waiting.
"...that this is what you really want?"
Lucrecia explodes into anger. Why? She urged him to ask what he wanted to ask, and she was holding something back before, while she waited for it. Is his eventual question not the one she wanted? Was she expecting a different question?
In Japanese, he seems to just stammer some more and maybe she's getting frustrated with him for that. But even then, it's like, "What are you trying to say? What are you trying to ask me? Just ask it."
And then her responses in English and Japanese are totally different. In English, she says, "Yes, I am sure," presumably meaning, "Yes, I am sure that this is what I want to do with my baby." In Japanese, she says, "This is my problem and by the way you're not involved in it," which seems to speak more directly to an implicit paternity debate. But even the English "Yes I am sure," which notably does not repeat the "sure about wanting to do this" part, might be intended to imply a different sort of, "Yes, I'm sure." As in, "Yes, I confirm what Hojo just said to you; I'm sure Hojo's the baby daddy and not you." As in language that is often used in issues of paternity along the lines of "sure," "certainty," etc.
And then Vincent kind of drops it and just mopes. In English he emits a feeble "I just," but in Japanese he seems to repeat the part that directly relates to him.
Then there's the weirdness about "just wanting to see it," but I'll chalk that up to poor translation meaning wanting to see her wellbeing or whatever.
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Anyway, that's all a *possible* interpretation. I'm not saying they necessarily meant all these things to mean all those things, because that would be kind of conspiratorial, but I
do think it's possible we were meant to wonder if they might have actually been hinting at a different issue than the one being outwardly discussed.
And for what it's worth, I only had to add one line at the end of it giving the whole thing context in order to actually change it into an indisputable paternity debate in my fanfiction.
However, I think this scene effectively quashed Vincent's belief that Sephiroth might have been his son, which is why by the time of FF7 he does not seem to be under that impression.
. That's why Hojo says that Cloud is misunderstanding, and that he's actually doing this to satisfy his curiosities.