No, it shouldn't. Most forums don't allow account deletion including post deletion, because it would destroy many threads and make it extremely hard for later visitors to follow the conversation.
Since HN doesn't require you to put any personal details, you can just throw out your email address and your account will remain as an empty hull holding the strings of your past conversations.
I am a staunch proponent of anonymity and privacy (hence why I post here under a pseudonym), but you need to make the decision about the level of privacy you want before you post. Changing your mind 1. screws over the community and 2. won't save you from the determined taking a trip through the wayback machine anyway.
However, if you're gonna be creepy about it, maybe I should be more proactive.
This would mean something a bit smarter than just replacing usernames with [deleted] though. Perhaps [deleted #nnn] or some other token.
Edit: and if you really wanted to get paranoid about ambiguity, generate a new token per thread rather than per user, making it all but impossible to correlate the entire posting history for a deleted account.
Also arguably, a thread for which a majority of users have deleted their accounts might not be worth following anyway.
I wouldn't really consider the deleted accounts to have worse comments. Especially for old threads... some users just retire their accounts, but the comments are still valuable when stumbled upon in the future.