This article applied to NT, but I'm guessing that the math is still the same:
http://support.microsoft.com/kb/q114841/
"NTFS uses 64-bit fields for all sizes, permitting its data structures to handle volumes up to 2^64 bytes (16 exabytes or 18,446,744,073,709,551,616 bytes).
This value is the theoretical limit for the NTFS file system. Practical limits having to do with the maximum allowable partition size described above limit the size of an NTFS partition to approximately 2 terabytes. Because the 32-bit fields of the partition table refer to the number of sectors in the partition, disks with larger sector sizes translate into larger permissible partition sizes. Currently Windows NT supports sector sizes up to 4 Kilobytes. With 4KB sectors, Windows NT can support a 16 terabyte partition. As new hardware or software schemes become available, NTFS will be able to handle substantially larger volume sizes."
If I'm reading this correctly, then, yeah, you'd need 4 KB native sectors to get to 16 TB partition size, and 512 Byte sectors will only get you to 2 TB. Note that the current WD "Advanced Format" disks all use emulated 512 Byte sectors, as far as I know.
This article:
http://mkp.net/pubs/lsf09-io-topology.pdf
says that, for now, Enterprise disks will come with native 4 KB sector sizes, while Desktop disks will come with the emulated 512 Byte sectors. The 3 TB disk that Seagate has "announced" will be an Enterprise disk.