The comments are public, and it's public knowledge which account they're replying to. What would be accomplished by encrypting them?

account -> email mapping isn't necessarily public, the email hosts transiting the email don't need that information leaked. it's about preventing info flow.

It doesn't look like you need to use the email associated with your account, though.

Yes, but even if HN knows you by me@example.com, and this fact does not leak, something else does: someone (probably you) is interested at getting replies to your comments at krapp@example.com. Deduction: that is one of your email addresses.

But email addresses aren't meant to be private, so even if that deduction is true, everything it appears to leak is still public knowledge.