JIRA has an inbuilt internal directory and external users can be created under internal directory.
You must ensure , you do not have projects with anonymous access, so that you can limit external users only to certain projects for which they need access to.
Another important aspect is tracking. Say, a customer A is an external customer and he leaves the customer org. You may need to remove his access ASAP (especially if your JIRA instance is accessible via internet).
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