How do deactivated users affect my license?

You can find more information in our documentation here along with details about licenses.

In short, no a deactivated user will not count towards your license count when it comes time for renewal. You can choose to manually deactivate these users via the System Console, Active Directory/LDAP synchronization, the CLI tool, or the server APIs.

If you'd like to see your user count you can do so via the System Console on the View Statistics page under "Total Users" in the Enterprise Edition.