Big fan of Zulip. Only problem is that you don't get email notifications unless you're directly @ mentioned in a response, even if you're participating in a discussion, and even if they're replying directly to you. Otherwise I find the threading approach to be a big win.
I'm working on a similar threaded messages project called Booklet (https://booklet.community), and I think good email summaries are the key to the product. It's hard to do, but there are some cool data opportunities to improve relevancy.