It would however cause users to start ignoring Twitter messages/notifications. People are already ignoring responses from people they don't know, and it can get even worse if we think most people interacting with us are just bots.
On the contrary - it does. Because the point of "favoriting" is that when my tweet is favorited, I expect that the other party liked it. Now that's not true anymore, since it could have just been a bot who performed that action based on keyword-targeting me, not by judging that the tweet has a value to be favorited.