There is no point in even putting together a botnet with thousands of CPUs anymore, a couple of FPGAs or an ASIC based solution would run rings around that botnet. Ok, an ASIC will cost a bit of money and a botnet is free but the difference in performance is such that only a very large botnet would be worth it and those can probably be monetized more effectively in other ways.

Botnets make a ton more money by just ad-clicks anyway. I bet its more beneficial to fraudulently ad-click with botnets than it is to mine bitcoins.