Building a sophisticated bot (like even the free ones are) requires a complete knowledge on how packets are sent and read, which must be learned simply by doing. Bypassing a commercial-grade "Hacking Shield", however, is public knowledge.
Bot developers also know more about the way that silkroad ticks than joymax does so they certainly have a better understanding than Ahnlab does.
So basically, no matter what security they implement the bots will work around it. The only way they can truly punish the bots are to either
A (What They're Currently Doing): Ban random players because 95% of the time they'll be botters
B: Have actual ingame GMs looking for bots and interacting with them to confirm whether or not it is a human.
However, in order for B to happen, joymax would have to care. And since GNGWC ends at the end of the month, soon they won't even be PRETENDING to care so yea bots will always live.