"Has steam screwed thye file structure up so badly that the install won't work anymore?"
I haven't tried installing HPB bot under Steam, but my guess is that Steam now has those MODs embedded in its gcf files. If the 'dmc' or 'gearbox' directories don't exist, then that's the case.
In the original Half-Life MOD system, there was a directory for each MOD at the same level as the 'valve' directory inside the 'half-life' directory.
With Steam, you have a directory with your Steam e-mail login and the third party MODs will all go inside that directory.
If you are using AdminMOD, then it would be easier to install the HPB bot metamod conversion that Pierre-Marie Baty made available.
See this thread for setting up the HPB bot with metamod on Steam...
http://forums.bots-united.com/showthread.php?t=777
P.S. AdminMOD uses metamod, so if you have AdminMOD installed and working, you already have metamod installed and working.
botman