We know what it means, but it’s still hard to distinguish at a glance what is quoted and what is not. It works in (plaintext) email because emails are traditionally word-wrapped and “>” is inserted at the start of each line – not once at the start of an arbitrarily long paragraph. And even then, email clients often color quoted blocks to further visually distinguish them.
Never had an issue with it on HN. 99% of quotes occur at the start of the post and the rest of the post is a reply.
Posts that interleave their content with quoted bits are rarely as constructive as they think (almost always just point-by-point bickering) that I find impossible to follow no matter what formatting they could've used for the quotes.
Also a single ">" prefix on a long wrapped line is a bit of internet convention with younger crowds probably thanks to 4chan. I doubt most people using it these days even remember seeing it in emails.
If anything, HN should post-process lines that start with ">" to indent them.