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this question comes from this post.

that post gives some equations and discussion based on those equations.

someone is asking for tag(s) about those equations.

You haven’t numbered your equations. Which one is “equation_1?”

for this case, which one is more appropriate to ask (reminder) someone to do something, "haven’t" or "didn't" ?

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Both are grammatical. There is no significant difference in meaning between these two sentences:

You haven't numbered your equations.

and

You didn't number your equations.

Both imply the reason for the next sentence, "Which is equation_1?" One uses the perfect tense to suggest B follows A, and the other uses the simple past to suggest B is due to A. It's two different ways to say the same thing.

There is, perhaps, a slight different in nuance. "Didn't" can be more forceful, like an accusation, so the person writing the comment might be trying to be polite. On the other hand, it can be mitigated in the usual way, by implying personal observation:

It seems like you didn't ...

It looks as if you didn't ...

I'm having trouble because you didn't ...

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