This got a bit long so bear with me lol.
I don't personally think that Knives's line in the scene you mentioned indicates that he's seen any black haired plants before the one we see him witness in the manga.
His line in that scene in Japanese is
"150年.… かかりすぎだ… おまえのお陰で足踏みのすえ更に多くの同胞が食い潰された搾るだけ搾り取られて最後はゴミ同然に殺され続けた仲間たちの姿"
If I were to translate it with more of the original meaning in tact I'd put it as:
"150 years... It has been too long... Because of you, and the time you spent stagnating/standing still, more and more of our brethren have been consumed, every last drop squeezed out of them. And in the end they were killed as if they were nothing more than garbage."
I think OH and DH use sight/seeing here because of the term "sugata" which can mean a variety of things depending on context such as form, figure, state, image, presence, role, character, etc. But usually if it was something specific that he actually saw with his own eyes and is describing he would say 姿を見た (sugata wo mita) or something along those lines. In this sense what he says comes across as a more general description of their state when they're killed rather than him recounting a specific event or events directly (though I'm sure he's thinking about the one he did see himself while describing it, I just think that informs his description of what the plants have been going through this entire time rather than it being what he is describing specifically).
Interestingly while OH translates the next line as "you don't get it Vash", in Japanese it's not explicitly clear if it's Knives talking or Vash. No one's name is stated, it just says "...それをおまえは知らない" or "that is something you don't know/don't know about". Dark horse even originally translated it as Vash saying "you have no idea".
If I were to translate it as Knives saying it, I'd say it comes across more as him saying that Vash doesn't care about what's been happening, or maybe that Vash is unaware, in which case Vash answers by expressing how he does know/care. If I were to translate it as Vash saying it, then Dark horse's translation as "you have no idea" fits well enough. And in that case he'd be following up by expressing his own experiences. Now it could go other way, if it was just the dialogue alone I'd say it's probably Knives saying it, but it being placed in a panel over Vash makes it less clear. Nightow's allergy to tails on speech bubbles isn't helping. So if I were to try to keep the neutrality, I'd simply translate it as "... you don't know anything." or somewhere along those lines, that way it could come from either of them and retain the same meaning regardless of who says it. But ultimately it doesn't change much about what's being said, just who is accusing who of being ignorant on the topic. I just think it's a funny bit of translation shenaniganery and wanted to mention it lol.
Vash's following reply is "亡くなったプラントは何度も見た「黒髮」だったよ寿命でなくなっていっただけじゃないんだな... 「能力」を限界まで使った証か... だけど... この砂の惑星で人間が生きていくのにほかにどんな方法があるんだろうプラントに...僕達に頼るしか方法はない..."
Which I would translate to "I have seen dead plants with black hair countless times. It's not the result of them reaching the end of their lifespan, it's a sign of their power being used to their limit... But... How else would humans be able to survive on this desert planet? They have no choice but to rely on plants... On our kind..."
And then it continues to him telling Knives that it's because of the great fall that they're all in this predicament, etc etc. Unlike Knives, Vash DOES use 見る here so he is talking specifically about something he directly saw over and over again. Knives' previous dialogue is more ambiguous and generalized. He has seen one dead plant in that state by then, but what he said doesn't particularly imply that it's something he's seen multiple times or seen before that point in the way that Vash's dialogue does.
To me this conversation comes across as Knives newly outraged over what he's recently found out that has been going on for 150 years while Vash sat around twiddling his thumbs (in Knives's opinion), whereas Vash has seen it many times before and thought about it in depth, even if he doesn't like the conclusion he's had to come to due to their circumstances (which are a result of Knives' actions). I think the subsequent lines where Vash talks about how only those who have actually experienced the suffering in question can talk about it and explain it to others, and say what needs to be said to stop it (paraphrased since I ran out of time to type out all the Japanese lol) seems to me like Vash is basically calling Knives out about how he doesn't get to tell Vash that he doesn't care and isn't doing anything and doesn't know what's happening when Vash is the one who has actually been in the trenches so to speak, seeing and experiencing this stuff and trying to bridge the gap between plants and humans. I think it also ties in well with Vash's "the reason you suck speech" in their final confrontation where he talks about how Knives loves to talk shit and jump to conclusions without ever bothering to try and learn about or understand where other people are coming from or what they're going through. Like with the village that he slaughtered in the scene where he cuts Vash's arm off. Knives takes refuge in ignorance while constantly talking down to Vash and accusing Vash of being the ignorant one. That's the impression I get from those scenes at least.
I'm not saying I don't think Knives ever visited his sisters, but I don't think he spent time with them or got to know them in the way Vash did, and I don't think he checked in on them consistently like Vash must have to have seen so many of the dead ones from final runs. I think Knives might have come swooping in whenever he sensed one in distress in his area, but I really don't think he had seen any of the black hair stuff before that point. He comes across as too shaken by it, like witnessing that happen was a wake-up call for him. If he had seen any dead ones with black hair in the past then he must not have thought about it or investigated the cause at the time, otherwise it wouldn't have blindsided him like that, but I don't think he would have dismissed it like that. Even if he hadn't gotten more involved before, he does still care about his own kind and would want to know what was going on with them of he noticed something off. So to me it makes more sense if he had never seen that stuff before and that's why he didn't think to investigate it before then.
I think it also fits the way he ramps things up so much so quickly, and why he acts so repentant when fusing with a plant for the first time. I think part of his anger, which he projects onto Vash, comes from guilt for not knowing about it sooner, for not being more involved because he was preoccupied with his own personal grievances towards humans. Another big aspect of his character that I think drives a lot of his actions is his isolation. Not only is he isolated from humanity but he's isolated from his own kind as well in a lot of ways. Even in the giant fusion he keeps himself separate, his sisters try to reach out to him in his dreams but he brushes them off. And the one person who was closest to him and who could understand him best had, in his eyes, chosen Humanity over him. Heck, the way his powers are presented visually is even different from others of his kind. I think in some ways he's lonely to a degree that even Vash has rarely if ever been, which only exacerbates his inability to cope with his fear and rage and feelings of betrayal.
I ran out of time before having to go to work, so I wasn't able to look through the Japanese version of the scene with the plant technician. But if you would like to talk about this sort of thing more then I'd be willing to go back to go over it when I get a chance if you're interested in that. But for now that's some of my thoughts on why I came to the conclusion in my original post.