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.
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).
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).