In what sense you not reply? No reply link? I noticed missing reply links on comments that are deeply nested. What you could do in this case is click the time link on a particular comment and you'll get to the reply form. Hope this helps.

No, after a while there is no reply link anymore, even if you click on the item directly.

I guess it is to keep discussions fresh and not have flame wars escalate, or something

It is to prevent necroposting. The reply button disappears after 14 days I believe.

EDIT: Oh you're talking about the max reply depth thing. I am not sure about that one, but I found the thread you mean and I can't reply to some of the comments that are deep enough. It seems likely that feature is about preventing huge flame wars.

Yeah recursion aint infinite on comments, it goes 3-4 levels deep and then comment button disappears

PS: You won't be able to reply to me directly as a 4th level comment I think

Yes I can. You can also just click on the link for a single comment and then reply there

Oh right

Flame war prevention mechanism I believe I've heard mentioned a few times. It's possible it might also stop derailing the original topic subject as well.