Is this the one that wasn't including transaction fees?
You must mean transactions, not tx fees.
I don't believe so, but the issue of not including transactions is far less serious than some give it credit for.
Mining empty blocks will at most slightly increase the time transactions take to get confirmed.
There are two larger risks botnets pose to Bitcoin:
(1) they could be employed to mount an array of disruptive attacks, possibly even the 51% attack
(2) they damage the economy creating downward pressure on the price. Unlike the honest miners, botnet operators can afford to sell their coins at $1.