There is no hard set limit on the number of customers or organizations that Service Desk can have in a project. Taken from the Jira Service Desk Evaluator resources:
Customers do not consume JIRA Service Desk licenses or JIRA user licenses. In other words, customers are completely free and unlimited.
The same is true of organizations.
That said, IF you're using LDAP to sync users into Jira, there are some known upper limitations before you would likely encounter performance issues. Check out Performance Issues with Large LDAP Repository - 100,000 users or more for more details, as well as Reducing the number of users synchronized from LDAP to JIRA applications. However this is specific to using a Connected LDAP directory that syncs on regular intervals as a means to manage users in Jira. You could alternatively use an Internal directory with LDAP authentication in Jira that doesn't constantly sync the user accounts as a means to get around this if you plan to scale to that level or higher with LDAP.
If you stick to just Jira's internal directory for these JSD customers, I don't expect you would encounter performance issues unless you were considerably larger than this in a single environment.
I hope this helps.
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