You have it all wrong, they are not shutting down any bots. The bots are sometimes interfereing with communication through blizzard because it runs through their servers but with different programs that are unstable. They want to change the system they have in the lobby so that bots will not be aloud to enter any other channel other than public channels and their own private channels. The third party isnt from the bots its from the servers they run through that are owned by the bot creators NOT the owner. For example if i was to own a bot and let it host games it would be using my i.p adress and i would be paying for it but it would need to use the servers from the place i got it (e.g M.Bot.) Most of these places are poorly made and the owners dont put any money into making them secure so people can easily make bots do whatever they want, which means that some people are making bots enter private channels and spamming. Blizzard wants to have all servers run directly through their own before being able to access battle.net and then they can reduce the problem.Added (2012-12-27, 6:37 PM)
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Not along ago they shut down all BGN bots and all ENT bots so they could no longer host but they got too many complaints and needed a better solution so put the bots back up.