Schema management in zookeeper has been the biggest pain point for us. Occasionally individual clickhouse shards will get out of sync during a schema update, which can be hard to diagnose.
We use a heavily modified version of clickhouse-backup[1], which works well for us.
As for hands-off replica reboot: you must have an automated process to reapply the same schema which exists in zookeeper, otherwise it won't resync. If the local schema gets out of sync with that in zookeeper, then you'll have issues again.
I expect a lot of these ergonomics issues will be fixed over time. It's already much easier to use than it was 3 years ago, and even if progress on usability and reducing the learning curve is slow the database performance makes it worth it.