After looking at the Matrix rules for 5th it seems like botnets aren't really a possibility anymore as devices lose all the marks they have once they reboot. So if you had a network of fifty slave machines they'd all be clean as soon as someone restarted them. Even if that is an infrequent occurrence it still seems like with RAW you can't actually build a botnet anymore.
Though maybe you could edit a file in the device to tell it to switch to a different set of operating instructions once it got a certain signal. A kind of "sleeper zombie." It'd probably be a one-time use thing but it sounds plausible.