Theres two things to consider:

First its cost effectiveness of banning Botting programs. Consider this: The game has 10 Botters who do the undercutting thing. They (to bot) pay 15 a month like everyone else. So SE nets 150 a month from these botters. Now of the entire playerbase, lets say only 3 people quit over the botter situation. Ultimately, for SE, leaving the botters nets them MORE money than it would to cut their accounts. You may not like that, but that is business 101 here. Sometimes businesses will allow certain activities to continue if it means greater overall profit.

Now, where this becomes flipped is if instead of 3 people quit, 30 people quit. Or 300 people quit. That drastically makes those 10 botters a huge negative in SEs profits.

Then we have to consider pragmatically what botters contribute to the game. We can argue that there are at least 4 different kinds of botters:

Lvling Botters - People who bot just to power lvl alts or other classes merely so they dont have to lvl.
Gathering Botters - Botters who just go about gathering Junk Non stop
Utility Botters - These would be botters who keep undercutting things by 1 gil
RMT/Spam Botters - These are botters who are doing RMT or spamming stuff.

OF those botting, The only one with a huge negative impact on the game at large is the RMT botters because they actively damage the economy of the markets as well as contribute to an indirect pay-to-win model that hurts the game. Utility Botters, while also a negative, dont damage the markets that badly to have extreme profound effects broadly, though theyre annoying at the individual level. And lvling botters dont really impact anyone else to much in open world content. Theyre oddities.

The wierd one is the gathering botters. They do affect market price, but they also create more supply broadly, which brings a really wierd predicament. Lets say that SE could wipe out all botters. No exceptions, and it would be permanent. One of the probably after effects of that would be prices would skyrocket on the MB. I do not believe the current amount of players who do active gathering/crafting would be able to support the demand the game would need. This would end up in shortages nad pricing out a lot of players from things that they were accustomed to getting.

Im not saying that farming bots are a-ok, but I think it would be foolish for any modern MMO company not to make proper assumptions that botting would be occuring and that it would be a factor in the games economy (and might actually be necessary for a stable in game economy frankly.) Thats a concept a lot of people dont consider, and see all botting as 100% wrong. Again, Im not advocating for botting, but rather that I do think the issue isnt a black/white thing.

As for taking care of botters currently, I dont actually encounter to many to often, and the most I see are the RMT ones. The fact that I dont see it to often to me points towards the fact that SE is actually pretty good at watching for botters of all stripes. The reason being that if they didnt, I could easily imagine how this game would look. And its not pretty.

I honestly dont think the 'bot issue' is the biggest problem with ffxiv as it were. A minor nuisance that SE keeps a close eye on is probably more accurate.