HyperThreading on Win2k is not supported because Win2k detects your single HT cpu as two CPUs. The reason this is BAD is that the system idle process, which is implemented as a NOOP in Win2k, will steal CPU cycles away from other running programs. This happens because a NOOP instruction competes with regular integer instructions on a HT cpu for the same resources. If you truly had two CPUs, this would not happen.
So I would recommend that you disable hyperthreading to achieve best performance in Win2k.
WinXP, on the other hand, recognizes the HT cpu and behaves accordingly.
Don't know if MS can fix this for Win2k... it would involve changing the kernel itself, which might affect regular system behavior and introduce problems into "legacy" systems. Microsoft is traditionally afraid to implement big changes like this because such changes tend to break the existing configurations...