As others stated, the reputation limit was added to prevent rep abuse, or more specifically, mass-downvoting. (Mass-upvoting was also a thing, but not as often/serious as the downvotes were)
It'd bring users that had 1000's of rep, down into the negatives pretty quick when abused. So the limit was added awhile back.
Doesn't have anything to do with bots.
While it doesn't stop mediocre rep abuse, this is something moderators can handle if notified.
Personally, I think the rep limit is fine.
Feel free to disagree though, I'm always welcome to discussing change if needed.