Recommended reading - Prevent an eventual PuppetDB slowdown - Preventative maintenance for PuppetDB: node-purge-ttl

For recent versions of PE, you can automate maintaining, backing up, and tuning your databases with the puppetlabs-pe_databases module.

If you'd like to prevent PuppetDB slowdowns in Puppet Enterprise 2017.2 and earlier, enable node-purge-ttl. Learn how from Nick Walker's blog post.