If you are already thinking about implementing – and have the skills necessary to implement – your own account system, then sending emails is probably not the hardest thing in the world.
The main problem, looking at the bare NNF, is that it is not build to store any data other than thread contents. For example, it doesn’t store email addresses of users. Mainly because its only storage is public RSS files and people might not want to make their email address public to all.
If the account system you are implementing contains people’s email addresses that would solve that issue. Having implemented your own account system also means you are already using custom code whenever a reply is submitted so it would be trivial to trigger the sending of an email.
One of the important parts is probably to not think about giving “updates from RSS files via email”. This is an unnecessary extra step. Instead something like this is probably what you want:
1. Let people subscribe to threads, store this in a database (you are probably using one for your account system).
2. When someone posts a reply to a thread your custom code kicks in:
2a. Check the name/password of the reply author against your database.
2b. Check your database to see if anyone is subscribed to the thread.
3. If 2a passes you:
3a. Save the reply to the RSS feed, as normal.
3b. Send an email with the reply’s contents to everyone subscribed.