I think the elephant in the room, ultimately, is that SE probably stands to lose money if they really crack down on bots. On one hand, bots probably pay more than regular accounts. They pay for a normal subscription, they often have multiple retainers, and they may support additional alternate accounts for laundering gil. From what I've seen, they also pay for job level boosters.

At the same time, you have a player base willing to put up with the problem. (Other than this thread, obviously)

If you ban 100 bots to avoid losing 1000 legitimate accounts, then you make more money. If you ban 100 bots to avoid losing 10 legitimate accounts, then you've lost money. I suspect that the latter scenario better describes the situation.