Hi Richard,
You seem to say that sites with more than 5 000 users can't use automated backups properly.
I can tell you that my main Moodle installation has currently 60 000 users account, with 20 000 active, and between 3 000 and 7 000 different people connected per day. Between 2 500 and 3 000 courses, and nearly 1 000 courses backuped (the other skipped) with automated backups in the night. My backups include user data and logs (old and new). My logs are kept 2 years (but courses resets each year).
I imagine that it also depends a lot of how your Moodle is used, what there is in your courses (big files, lot of quizzes attempts...) and the power of your server, and how it's optimized.
Concerning backups, i've configured them to use a dedicated specified folder, and use manual launch (not automatic), skip hidden courses, and skip non modified courses from 60 days.
Then, i use a dedicated cron job to only launch the automatic backup script (admin/cli/automated_backups.php), allowing a lot of memory for PHP, and unlimited time (really 36 000).
Another important thing : i've made a modification in backup/util/helper/backup_cron_helper.class.php to ignore (not backup) the course 1 (Moodle's main page)!
I hope these information can help you to make your backup works well. If you need more details, ask and i'll try to help better.
Séverin