Running two puppetdb in front of a single postgresql here and it's fine. The puppetservers use one puppetdb for everything and the second puppetdb is for monitoring and interactive use. The only hiccoughs are when trans-oceanic links blip.
The puppetdb instances are managed using puppet and at my SLA levels I get to shrug and say that agent runs will fail for a minute or so during the upgrade. Depending on your SLA you may have to upgrade at a specific time or swap servers behind a load balancer or something else quicker.
If I had a tighter SLA I would build new upgraded puppetdb hosts instead of upgrading in place. (Then repoint the puppetservers and turn down the old puppetdb hosts.) I haven't had schema issues during puppetdb upgrades.
For the puppet 4->5 upgrade I have a new 1xPostgreSQL9.6+2xPuppetDB5 set built, the upgraded puppetservers will fill them up soon enough.
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