I think it definitely hurt Jagex's profits in the sense of subscribers, but I think numbers will grow in time. Now that players aren't immediately facing spam from gold websites when they join the game, I think new players will stick with it. If I joined and saw all that spam, I would consider this game not to be controlled and dying and wouldn't continue playing. I wouldn't consider the bots that "played" RuneScape players at all. So in a sense things really haven't changed.
Congrats on 99 smithing btw :].
Congrats on 99 smithing btw :].