Looks like reddit got the answer;
https://www.reddit.com/r/mysql/comments/r50yor/mysqldump_new_problem/
For some reason all databases fails the whole backup silently. This might be a bug in mysqldump? None of the guides I'm reading mention this not working. I have to specifically tell it what database I want now.
This works; mysqldump --no-tablespaces --single-transaction --quick -p -u zabbix zabbix > ~/backups/full-backup-$(date +%F).sql
Background info;
mysql> show databases;
+--------------------+
| Database |
+--------------------+
| information_schema |
| zabbix |
+--------------------+
2 rows in set (0.01 sec)
mysql> SHOW GRANTS;
+------------------------------------------------------------+
| Grants for zabbix@localhost |
+------------------------------------------------------------+
| GRANT USAGE ON *.* TO \zabbix`@`localhost` |`
| GRANT ALL PRIVILEGES ON \zabbix`.* TO `zabbix`@`localhost` |`
+------------------------------------------------------------+
2 rows in set (0.00 sec)