Interesting. The "reply" link is hidden for some comments - but not others - such as this one, yet I am able to bypass it by modifying the "reply" URL. Is this something new, or simply something I hadn't noticed before?

Just click "link" above the post and the reply box appears.

Right. Hm. I wonder why it does that.

To slow down deeply nested short responses because they tend to contribute little to the overall discussion.

This thread is an example of why the delay is implemented, and this comment is an example of low value comments.

Save space. If it had to have a "reply" button after every reply in a large comment block it would not be able to fit very many comments on the page.

They really should scrap the reply link entirely and move it next to the "flag" button e.g. | reply

Mm, can't be that. If you highlight the area under the comment, there's a row of dashes ("-----") where the "reply" button should be. It takes up the same amount of space.

And the karma limit is intended to ensure that the people who take this quite expected action have good taste.