There’s no obligation to use the Agile Hive issue type schemes - you can use none, all, or a subset of them. You can also add / remove issue types from any of the schemes as needed.
Agile Hive issue type schemes can be recreated by a Jira administrator at any time if deleted.
Agile Hive issue type schemes require Agile Hive Issue Types in order to be fully available: OLD Manage Agile Hive Issue Types
If not all Issue Types are available when creating an Issue Type Scheme, the scheme will be created with only the issue types available.