notwithstanding ntop's non-supportive moves wrt the ntopng plugin, if anyone is having odd periodic WAN and/or LAN losses and is running ntopng with active network discovery, it can be solved by turning off ntopng active network discovery or by going to your opnsense web-interface->services->ntopng->settings and setting interfaces (may need to click advanced) explicitly to EXCLUDE WAN (i.e. add any interface but WAN. Or remove ntopng :D.
This seem to be the solution for ntopng community from opnsense or if you install via ntop's repository.