I think those last names were made up by fans who wanted surnames for characters in their fanfiction. A fair amount of people agreed on those decided last names, in order to provide a little continuity in fanfiction as a whole.

Yes, as for Hojo, does anyone know if in Japan, Scientists/teachers are refered to by their first or last names? I'd assume last names because look as 'Instructor Trepe'. But then again, thete's also 'Headmaster Cid', not 'Headmaster Kramer', and there's 'President Shinra', as they don't mention the guys first name. So I haven't a clue, but overall, Hojo is probably Hojo's last name.

As for (SPOILER)Vincent being Sephiroth's father, that's quite debatable. It's a nice thought for people who want to think Sephiroth wasn't (SPOILER) born through rape/forced sexual intercourse/sex that is not for love, and also, from an unloving father. Not to mention the fact that I personally think Lucrecia + Vincent = Sephiroth, looks wise more then if we switch Hojo into the equation.

All that considered though, I don't think it is possible. At least when we play the game in English, in NA, it isn't made obvious, or possible. For all I know, it could be the same as FFVIII, where in the Japanese game, there is no doubt, and it is specifically stated that (SPOILER) Laguna is Squall's father. But in our version of the game, you have to pay attention to some subtle scenes and happenings to know that.

I don't personally believe that (SPOILER) Vincent is Sephiroth's father, but I can see how other people might get that idea.