Windows NAP Operating System compatibility

Yes, NAP is deprecated in Server 2012 R2. Network access protection being deprecated does not mean it's not a viable solution anymore, and in fact, is fully supported in Server 2012 R2 and Windows 8.1. Being marked as deprecated simply means that it's being phased out, and therefore will not be available in some future release. (They haven't yet specified which future release this will be - could be the server version of Windows 10, could be the one after that, etc.)

As to why it was deprecated, you'd have to ask Microsoft to find out for sure, but there's a decent blog article on the deprecation at Windows IT Pro on the subject. The three reasons they list, which I also believe to be "why," are: low adoption rates for Windows NAP, the existence of better solutions to the problem that NAP addresses and the incompatibility of Windows-based NAP with BYOD policies.

To answer your question about client management, it depends on what you mean by client management:

NAP Client Configuration can be used to configure NAP-capable computers only. A computer is NAP-capable if it has the NAP components installed and it can verify its health by creating a statement of health (SoH). Computers running Windows® 7, Windows Vista®, Windows XP Service Pack 3 (SP3), Windows Server® 2008, and Windows Server® 2008 R2 are NAP-capable. You cannot use NAP Client Configuration to manage computers that are not NAP-capable.

If you mean you actually want manage/administer the computers with the appropriate MMC snap-in, you should be doing your administration from a computer running a version of Windows which is the same or higher than the computers you're trying to administer. So, if you only have XP computers, you'd need Server 2003 or higher or a workstation with XP or higher, and the appropriate remote server administration tools (RSAT) installed. If you're trying to manage a Windows 8 client, you'd want Server 2012 and up or Windows 8 and up, with the Windows 8/Server 2012 RSAT pack installed.