Botnets are the matrix equivalent of sending a hoard of guys with knives into a gunfight. Every agent in a botnet can be commanded at once, but has to roll individually. Generally bots are next to worthless, on account of they're running on low-level systems and the weight of the agent's programs is likely to drop their effective response to nothing, so they'll be throwing 2 dice for initiative, if you're lucky, and attacking with maybe 4. Really, it's best used as a distraction.
Rules are in Unwired. p100
They are spread using the rules for mass probes, (detailed on p99,) and take a lot of minding to stay powerful.
Still, like today, they can crapflood the hell out of any node and keep whole teams of spiders busy.
