The platforms work a bit differently when it comes to plugins. I know that all Atlassian Cloud accounts will have at least one user account that is used on the Cloud platform in regards to plugins. But it sounds like you might have a lot of different user accounts, which is possible depending on what plugins you were using in Cloud.
I believe you should be able to deactivate those user accounts once you are on the Server platform. We would recommend against deleting user accounts in Jira, because it tends to cause more problems from a historical data point of view. But to mark an account as "Inactive" will remove them from all licensing seats and prevent that account from being able to login.
That said, it might be possible some plugins on server might need a user account to work correctly. I don't know of any such server plugins that do this personally, but I suppose it might be possible. So while yes, I believe it's safe to deactivate those users, it's probably worth testing your server plugins to make sure they are working correctly after this migration (should the vendor also have a server version of the same plugin).
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