It's probably expected for a botnet of this size to be rather "global".
"116,000-bot-strong operation devoted to Bitcoin hacking and other crimes"
this was not the first botnet discovered using this Kelihos software. sounds like there are multiple operators using it.
This, plus the possible "iMine" software make me think that there is a botnet mining pool operator somewhere, allowing botnet operators to connect. If, indeed, there are more than a few botnets using such a pool, it might be hard to notice if just one botnet went down.