I would greatly enjoy a comment-reply alert. Having to check my profile again and again to manually detect replies is not super efficient. Often I discover replies too late to engage an already gone replier.
In the meantime, I do suggest trying hnreplies as sloppycee suggested. Unless you comment here a lot, it's not that many emails - and it has the advantage that you don't have to keep watching or reloading HN to see if you got any replies to a comment.
Considering how fast stories drop off the home page, hnreplies gives me a chance to reply to a comment while people may still be looking at the thread.
So give it a try - you can always unsubscribe if it's not for you.
Reddit does it perfectly. You see alert and get ALL unread replies and pop them with a simple body click.