I hardly ever reply within hubs anymore. I do all my comment moderating and replying from one global place under my account - hubs - comment page. It's easier and no need to go into each individual Hub.
The reply button is still there in the global moderation page. But you are right, it vanished from the comment capsule. If you still moderate directly in each Hub, you can still reply by adding your own comment, but only once.
HP just added a nice feature where we can reply to each answer in the Q&A (where we are now - see the blue comment link?).
It seems that when they put that in, it was the same time that the reply option was lost from the hubs. Just my guess, not sure on the timing or even if one had to do with the other.
But I wonder if HP is in the process of adding the same feature to the hub comment capsule as we have now in the Q&A. This might explain why it was removed for now. Might have been a code conflict. And if so, they might be working on adding it to hubs too.
This will be great if we have that feature in hubs to have our reply attached to their respective comments.