How can "HierarchyID" type work when "CLR" is disabled?
The clr enabled server configuration option only controls whether user assemblies can be run by the SQL Server instance.

The hierarchyid, geometry and geography types are system CLR types. These are contained in system assemblies, so are available regardless of the clr enabled setting. 

Similarly, other system features that rely on CLR integration, like FORMAT (SQL Server 2012 onward) are available even if clr enabled is off.

If you need to manipulate hierarchyid data in a custom CLR routine, you will need to enable user clr assemblies via this setting.

See also: Hierarchical Data (SQL Server)