Here we go....
dcane2000, the extra security features do add overhead but due to the more efficient handling of files by NTFS it doesn't run slower than FAT. Benchmarks have the two running neck and neck. As a matter of fact when accessing large directories and partitions NTFS is faster, noticably and benchmark-wise.
The base version of NT 4.0 and W2K do run different versions of NTFS. However SP5(It may have been SP6, I can't remember off the top of my head) upgrades NT 4.0 to where it can use NTFS5 which is what W2K uses. There are some features that are not accessable in NT 4.0 such as Disk Quotas, but NT 4.0 is with compatible with NTFS5 in this manner.