A big benefit of the organization provided by every message being in a topic is that it makes finding this more efficient. E.g. if you remember that Steve made a joke about donuts in the conversation, you can search for messages sent by Steve mentioning donuts, find the topic, and from there find the actual conversation. I do this to find months-old or years-old conversations several times a week.

If you're curious to hear more, https://monadical.com/posts/how-to-make-remote-work-part-two... talks about this idea in more detail.

I also highly recommend making use of Zulip permalinks to conversations in issue trackers and other resources -- my anecdotal sense is most projects using Zulip do that a lot (the Zulip development team certainly does). Certainly the main feedback we've gotten on the zulip.com domain transition is "Will my permalinks keep working???". (Yes, they will).