I am thinking about buying the JIRA service desk on top of my JIRA Agile. Does JIRA Service Desk customers count against JIRA Agile users? I cannot seem to find this already asked somewhere.
No.
Service Desk looks at "Agents" (who are also JIRA users), not customers.
Jira, JIRA Agile and most other plugins just look at JIRA users, not customers.
As reference for Nic's answer: - https://confluence.atlassian.com/display/SERVICEDESK/Customer - https://confluence.atlassian.com/display/SERVICEDESK/Managing+customers
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Please read the links Charles gave you.
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