Have they stated the justification for this anywhere? You'd think a site that brands itself as being for hackers would value its users having control over their comments/privacy.

There's value in editing for clarity within a window of a live discussion. After the live discussion is less active, it's important to be able to reference things or see a coherent view of the discussion and what people were responding to.

Yes, it's because the comments create a discussion thread that then becomes impossible to follow (or worse, misleading) if certain comments within it are either deleted or edited to say something different. The idea is that what you write becomes communal property once it's been responded to, because it's part of a community discussion that loses meaning if people start deleting individual comments.

I believe that, even within that two hour window, you cannot delete if anyone has replied to it.

You can still edit it to say "[deleted]" or something, though.