Since you've mentioned twice that you didn't get an explanation, I'd be curious to see the case that you didn't get an explanation about. Is there a link? Usually when people remain upset about something long after the fact, it's for good reason.
It doesn't really depend on whether I think someone's trolling, because the response is usually much the same in either case and anyhow genuine trolling (i.e. totally bad-faith action to provoke or waste time) is relatively rare.
I've sent a lot of HN mod mail over the years, and usually get a response within a few hours. Occasionally a few days, during busy times, and on a very small handful of instances, an apology for missing or overlooking an email. I think all of those have occurred within 1--2 weeks tops.
I try to keep most correspondence short, sweet, single-focused, and direct. (Most of that concerns submissions: titles, URLs, or nominations to the 2nd chance pool.)
Occasionally I address more complex or difficult issues. Dang emailed me a few days ago noting that he's still meaning to reply to series on one topic (not pressing, though interesting). I'm aware that he's pressed and that there are more urgent priorities. But he does go out of his way to stay on top of things.
(I also owe him a reminder on another issue, also fairly minor, I'd raised a couple of months back.)
Keep in mind that mods are ingesting a firehose and that complicated or poorly-scoped questions or issues might be difficult to respond to. (This is a general principle to keep in mind when corresponding, not just for HN mods.)
I have no desire to take HN "offline" and pollute my inbox/outbox with a bunch of moderation notes. That's too annoying.
It might be slightly better if every submission and comment had a mailto: that automatically populated a new email with a link, but even then, this shouldn't be necessary.
I don't think you need to go back and forth with users. You don't actually need to do anything - this is just my opinion.
I do apologize if it caused you any grief, that wasn't my intention either.