I read it as "it" being the situation. e.g., "was it a child who painted this?"
it isn't bad grammar, though you could argue it's poor writing because it's confusing. it's using a feature of english called it-extraposition. some examples here: https://www1.icsi.berkeley.edu/~kay/bcg/extrap.html
basically, it-xp lets you delay a constituent in certain circumstances using "it". sometimes this is required to make a sentence grammatical.
"(What to do next) is not clear"
"It is not clear (what to do next)"
*"Was (who painted this) a child?"
"Was it a child (who painted this)?"
We can combine this feature with clefting the end of the sentence to make something that seems to refer to a person by "it", but actually refers to an elided constituent:
Discourse: "I don't know the gender of the writer"
R1: *"Was (who wrote this) a man?" (can't have wh-phrase here, needs it-xp)
R2: "Was it a man (who wrote this)?" (OK, but the last part is redundant. Discourse already includes we are talking about a writer. Grice's maxims suggest we will usually drop it.)
R3: "Was it a man?" (looks weird, but sounds perfectly normal in context)
I'm a linguist / syntactician by training, but also nonbinary and use they/them, so I have some skin in this game. I think the GP was being obtuse, maybe purposely, but not malicious.
Fair enough. It might have been the usage combined with the rest of that user's posts, which seemed to have an aggressive tone, that caused me to read it the way I did.
I will also say it is worth the tiny bit of extra effort to make pronoun use clear when dealing with members of the trans people. That community already faces so many challenges, accidentally offending them with our laziness is a mistake we shouldn't make.
That is fine, but keep in mind that a valid answer to that question can be “No, it was a cat that did it.”.
If you are already sure it was a person and wanted to be specific, you could rephrase that as “Was the person who did this a man?”.
(The answer to that might of course be “I don't know, they looked rather androgynous.” or the more down to earth “Dunno. Couldn't tell if it was a bloke or a gal.”.)
I wrote a more detailed answer to GP: https://news.ycombinator.com/item?id=24576616, but basically: yes that's totally natural, but in edited writing / speech sometimes should be avoided for clarity reasons. But I didn't blink twice at the comment myself.
Maybe that also isn't intentional and is merely poor grammar, but that certainly reads as if you are using "it" to refer to the person.