For example, our developers are JIRA agents, but would not but utilizing the Service Desk add on - when calculating the licenses we need for Service Desk, do I need to count the JIRA agents who will not be using Service Desk?
Yes, but no.
Each person who needs to be an Agent in Service Desk needs a licence. If they do not need to be an agent, then don't make them an agent. A "JIRA Agent who will not be using service desk" is pointless - they don't need to be Agents, so drop them out of the Agent group and they won't count. I think you need to decide whether your developers really are agents or not.
I believe it depends on Service Desk version you use. In SD prior to 2.0 you had to match your SD license with your JIRA license but starting with SD 2.0 Atlassian introduced new licencing scheme:
There NOT everyone who is JIRA user has to be agent in SD but only people who work on customer issues.
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