One important hack - Q3InfoBoom - operates entirely out of the scope of the vm
Which means Twifire cannot counter it.
To protect your server, I give you jk2mp2.exe - a modified version of jk2mp that can resist Q3InfoBoom.
Simply use it exactly how you would jk2mp.exe... but only as a server. It doesn't work well for actually playing the game.
To use it, you must copy it into your JK2/GameData folder.