Hi, I haven't had a good look at the new SDK yet. But first of all I'm not sure if the "Orange Box" SDK will work with older MODs (I'm guessing it should but I could be wrong).
You can catch the MOD by checking the names of the current steam/game directory, that's about it.
The example bot that you get with the new SDK is still braindead, you have to select its weapon/behaviour using console commands, not exactly autonomous
I think the NavMesh stuff requires the old GAME_DLL hack to compile If I remember right, even then I don't know if it will work with server plugins.
Basically the stuff that marD mentioned is obv. still required. Although to develop bots in any MOD requires some sort-of interface to the rules of the game also. Such as in TF2, we need to know where the capture points are, what capture points are locked, sentry gun level, if a medic is currently healing a bot or not, determining spies disguises and so forth... I don't beleive theres any simple way of finding this out.