After careful, diligent curiosity I have found that 30% of the players of this game are unrepentant hackers that somehow don't get perma-banned by Nexon.
After further diligence I have discovered that some of the end-game bosses are mathematically, scientifically impossible to complete without hacking. Thus, Nexon requires hacking at end-game. So learn how to hack. Nexon loves it.
Botting is typically a hex editor or cheat engine thing. Most times it's done by tampering with the signal between the client and server but sometimes it's just messing with the client. This is part of why so many people get Legendary Potentials so fast. They force the cube to upgrade the potential and go from Rare to Leg in 3 cubes. Then they force the Starforce to Success each time. Then they bot like mad and meso farm ultra fast because every monster is sucked to them, they cannot be hit by monsters, and their pet soaks up all the goodies at light speed.
Nexon could watch for critters in "unauthorized" or "abnormal" locations (there aren't many classes that mess with mobs' map location and they are limited in where they can move the mob) and flag the map that it's happening on for a GM to have a look. They could also look for "excessive looting patterns" that are impossible in legit play (such as uninterrupted meso grabbing over a period of 30 seconds) and kills that happen too fast for too long a period (e.g. 2 or more kills per second with no interruptions for 30 seconds). They could flag certain characters as "legit badasses" so they don't constantly get drawn to the maps that they are wrecking mobs on while keeping the detection on high sensitivity to pretty much instantly pick up on hackers/bots.
There are many ways to go about it and most of them are small scripts that use very little processor time. Nexon just doesn't want to catch botters is all. They like hackers. Otherwise this game would have a LOT less of them. "Just don't get caught" seems to be their motto by what I've seen. I could be wrong though and Nexon could just not want to chase hackers down because they would rather make more content instead.