Possible case could be a locking of some server thread. You can capture server threads when you see delays in working with the server from the GUI, here's the script: https://github.com/netxms/netxms/blob/master/tools/capture_netxmsd_threads.sh
Script should be executed 3 times with 20-30 second interval. It needs gdb and netxms-dbg packages installed on the system.
Also to check - on netxms server node there should be Server: Number of Processed Events (based on internal Server.TotalEventsProcessed metric) - just to verify that there we no sudden spikes in event quantity.
In overall there's quite a few metrics there, e.g. Server QueueSize ones, it's worth checking them for any big spikes.
If you don't have Server.ImportConfigurationOnStartup set to Always, you might not have the most recent template with above mentioned DCIs, you may want to import them from /usr/share/netxms/templates/netxms_server.xml