It's mostly the implication that "lost both a mother and a brother to evil twenty years ago" means that both Eva and Vergil suffered the same fate and the same time. Plus, Trish being the servant of the dude who made that happen, it's really easy to come to the conclusion that everything was trying to imply they both died :/ Given the context of only DMC (no other knowledge we have from the series as a whole), there's no way to interpret "lost both a mother and a brother to evil twenty years ago" other than them both suffering that same fate. There's no implication of Vergil "falling to evil" that makes it different from how Eva was "lost to evil." Both are said to have been "lost to evil" in the same breath, and then every other mention of that particular event talks about how Eva was murdered, which would seem to imply that Vergil was murdered too, having suffered the same fate. Even in general, the two being "lost to evil" is just a flowery, archaic phrase they wanted to use to make things sound a bit darker and dramatic, and inadvertently fueled the assumption. If they didn't want us to think Vergil wasn't murdered in the same event as Eva, then they shouldn't have used that phrasing, but then it would ultimately let us know that Vergil's fate is unknown, and make identifying Nelo Angelo that much easier.
Dante often referring to Mundus' atrocities toward Eva, but leaving out mention of Vergil is mostly to place a lot of emphasis on how much Dante cared about his mother (her being the catalyst for his human compassion and all), and to not consistently bring up the brother at all in order to make the big ol' "Nelo Angelo is Vergil" twist come out of nowhere - a twist isn't as great when we see it coming, after all. The more they mention Vergil, the easier it would be to come to the conclusion about Nelo Angelo on our own, lessening the impact the reveal was supposed to have.
It's murky, and mostly just sh!tty writing on their part.
Although, when you think about it, the DMC1 game and novel are pretty much self-contained, being the only things that Kamiya closely worked on. DMC3 had his collaboration, but it was still Itsuno's show. All in all, the DMC canon is still f#cked because of all the hands it passed to :/
Whatever.