Yes. But as dang says every so often, don't reply to a bad comment with another bad comment. This "I know you're not that stupid" thing is obviously not necessary. Leave that out and we wouldn't be having this conversation about what's acceptable and what's not.
That's a good point. That said, 'I know you're not that stupid' is one way of addressing a concern: it's a more humanized, more personal way of calling out a significant criticism that's worth making.
Another would be, "It looks like you are trying to plant the assumption that there are no possible Twitter users serving as puppets directed by others. Taking your statement at face value with best faith interpretation would lead to abandoning the whole discussion and trusting whatever goes on at Twitter to be just plain organic population, but we're pretty sure that's not the case. Why are you making statements that strongly suggest all of Twitter is just organic userbase, and minimizing the very thing we're talking about? We're literally talking about bots here.'
That's a lot wordier than 'I know you're not that stupid', and a lot less personal. Is it better? In some ways it implies the bot-minimizer is actively taking a role as a bad actor, not merely being foolish. I think such actors exist and also post on Hacker News and more or less everywhere else, but it's a nastier accusation and 'you're not that stupid, so what gives?' is a much gentler way of addressing it.
Especially when talking about use of, and restraint of, social media bot networks (AS THE PRIMARY TOPIC, I might add), we have to be able to talk about good faith and bad faith. It's literally the point of the whole discussion.