There is no difference between a win2k and winxp bottle, other than the windows version reported. This is almost completely true as well for win98 bottles, except that Wine emulates very few win9x specific behaviors in a win98 bottle, like not triggering an exception on a privileged instruction.
Unless Steam and HL2 behave differently when they find that winver = winxp, there is absolutely no difference between a win2k and winxp bottles for the games, so there should not be a performance difference. About two years ago we made the Steam installer prefer a win2k bottle because we generally use the oldest windows version that the app fully supports. Unless Steam somewhen refuses to run in Win2k, there's no need to change it, but I think that we'll switch to a windows vista bottle as soon as we have a d3d10 implementation.