Well, for starters, it's unlikely that SE much cares about the troupes of THM/ARC parading around. These bots are the smallest of the small fry; they can be recreated in seconds, so banning them is like spitting up a waterfall. It's MUCH more effective to ban these bots after days or weeks of work has been put into leveling and equipping them. Not sure what is meant by "strengthening the areas"; bots interact with the game in the same manner that players do. It is pretty much impossible to tell whether a command originates from a player or from a computer - because player commands also originate from computers.

Additionally, they are low priority because the only folks they bother are the folks who can't stand that RMT and bots exist in any form. For everyone else, they barely are even aware that they exist. The only times you're likely to even see them are at low levels while they grind mobs until they're high enough to enter dungeons. They don't monopolize any resources that are desired by players. They don't speak or interact with players in any way. Stamping them out is pretty much impossible, so SE leaves them alone until they get to the point where banning them actually has some sting.

Tellbots and shoutbots are another story; SE jumps on them pretty quickly. It's extraordinarily rare that you'll see a tellbot last even as long as a full day. Unfortunately, doing so is just as pointless as taking out the leveling bots: they can be and are replaced in seconds. Nevertheless, SE eliminates them as fast as possible in order to appease players who don't understand how impossible a task it is to stop them entirely. (There are whole forum threads full of hilariously bad player suggestions as to how they could actually be stopped: Ban all Chinese IPs! Stop all player communication until you ding level 50! Autoban any player who sends a tell to more than five different people in a minute! Those are some of the worst I've seen, but I could go on...)

SE's primary targets are ones that are less visible to players; the ones that store and distribute gil. These are the ones primarily involved in the actual business of selling gil to players, and these are the ones that hurt RMT most when they get banned. Finding these is another reason why SE tolerates leveling bots: by tracking where the leveling bots send their gil, SE can figure out which bots are storing that gil. A properly aimed ban can cost RMT billions of gil, something that stings far worse than cleaning up a pack of THMs and ARCs would.