The mbeans names seem to have changed with puppetdb 4 and thus we'll need to update the whitelist used by jmx_exporter.
Asking for a list of metrics to jmx_exporter returns only generic metrics, not any puppetdb-specific metrics, suggesting the mbeans names have changed:
root@puppetdb1001:~# curl $HOSTNAME:9400/metrics -s | grep -v '^#' | sort
jmx_config_reload_failure_total 0.0
jmx_config_reload_success_total 2.0
jmx_scrape_duration_seconds 1.25084E-4
jmx_scrape_error 0.0
jvm_classes_loaded 20318.0
jvm_classes_loaded_total 23497.0
jvm_classes_unloaded_total 3179.0
jvm_gc_collection_seconds_count{gc="PS MarkSweep",} 7.0
jvm_gc_collection_seconds_count{gc="PS Scavenge",} 1973.0
jvm_gc_collection_seconds_sum{gc="PS MarkSweep",} 1.175
jvm_gc_collection_seconds_sum{gc="PS Scavenge",} 27.297
jvm_info{version="1.8.0_151-8u151-b12-1~deb9u1-b12",vendor="Oracle Corporation",} 1.0
jvm_memory_bytes_committed{area="heap",} 1.876426752E9
jvm_memory_bytes_committed{area="nonheap",} 3.17964288E8
jvm_memory_bytes_max{area="heap",} 5.726797824E9
jvm_memory_bytes_max{area="nonheap",} -1.0
jvm_memory_bytes_used{area="heap",} 6.02389992E8
jvm_memory_bytes_used{area="nonheap",} 1.89071312E8
jvm_memory_pool_bytes_committed{pool="Code Cache",} 5.996544E7
jvm_memory_pool_bytes_committed{pool="Compressed Class Space",} 6.0096512E7
jvm_memory_pool_bytes_committed{pool="Metaspace",} 1.97902336E8
jvm_memory_pool_bytes_committed{pool="PS Eden Space",} 1.21634816E9
jvm_memory_pool_bytes_committed{pool="PS Old Gen",} 6.33864192E8
jvm_memory_pool_bytes_committed{pool="PS Survivor Space",} 2.62144E7
jvm_memory_pool_bytes_max{pool="Code Cache",} 2.5165824E8
jvm_memory_pool_bytes_max{pool="Compressed Class Space",} 1.073741824E9
jvm_memory_pool_bytes_max{pool="Metaspace",} -1.0
jvm_memory_pool_bytes_max{pool="PS Eden Space",} 2.096103424E9
jvm_memory_pool_bytes_max{pool="PS Old Gen",} 4.294967296E9
jvm_memory_pool_bytes_max{pool="PS Survivor Space",} 2.62144E7
jvm_memory_pool_bytes_used{pool="Code Cache",} 5.8537472E7
jvm_memory_pool_bytes_used{pool="Compressed Class Space",} 2.6088464E7
jvm_memory_pool_bytes_used{pool="Metaspace",} 1.04445376E8
jvm_memory_pool_bytes_used{pool="PS Eden Space",} 1.5145872E8
jvm_memory_pool_bytes_used{pool="PS Old Gen",} 4.38382048E8
jvm_memory_pool_bytes_used{pool="PS Survivor Space",} 1.2549224E7
jvm_threads_current 69.0
jvm_threads_daemon 27.0
jvm_threads_deadlocked 0.0
jvm_threads_deadlocked_monitor 0.0
jvm_threads_peak 79.0
jvm_threads_started_total 11996.0
process_cpu_seconds_total 2686.74
process_max_fds 4096.0
process_open_fds 114.0
process_resident_memory_bytes 2.167627776E9
process_start_time_seconds 1.520530381391E9
process_virtual_memory_bytes 1.2579303424E10