There seems to be a misunderstanding of what is a discovery rule and what is an item prototype, so I shall try to explain.
Suppose you create a discovery rule to discover network interfaces on a host: net.if.discovery. That discovery rule (a real item) is processed every "delay" seconds by contacting Zabbix agent.
Suppose you also create an item prototype to graph incoming traffic for every discovered interface: net.if.in[
,bytes]. The prototype itself is not processed by the server.
Suppose then net.if.discovery discovers a bunch of interfaces on a host. Several real items are created from item prototypes: net.if.in[eth0,bytes] and net.if.in[eth1,bytes]. These two items are processed by Zabbix server.
Summarizing, item prototypes are not real items and do not gather any data. They only serve as a template for real items, created as a result of low-level discovery. Discovery rules should count towards queue, but item prototypes - no.