It is possible to configure apm-server to drop transactions sent by agents marked as non-sampled:
apm-server
sampling:
keep_unsampled: false
By default, non-sampled transactions are kept. We will flip the default in a future release -- probably 8.0. In the meantime, we should document this configuration so users can opt into dropping them to save on storage. For the UI to report metrics (such as throughput) correctly this requires "Metrics-based UI" to be enabled in Kibana, i.e. xpack.apm.searchAggregatedTransactions should be auto or on.