Thanks for your reply spuluka. I will try to enable logging to file which I can later attach to this topic.
As written in KB article, 0 option should disable traps on LLDP and that option works on most switches (but not on EX3300 with Junos 15). Default option is to send the traps and you can't delete the command if you don't have it in configuration. If you have it and delete it, the option returns to default which is to send TRAP on LLDP every 5s.
[edit protocols lldp]
root@EX# delete ptopo-configuration-trap-interval
warning: statement not found
{master:0}[edit protocols lldp]