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In response to your questions:

1. If you want to do any sort of geometric reasoning about your scene, then autofocus is absolutely taboo. Auto focus changes the intrinsic camera parameters and thus makes estimating high quality metric scene geometry near impossible, and definitely not real time. The typical workflow with stereo cameras is that they are manually focused and rigidly aligned specifically for the type of scene, calibrated and then unchanged.
2. Autofocus may not have any effect on object recognition depending on your detector type. If it uses only 2d image information, then this will likely have little effect, but if the detector requires 3d information then autofocus will prevent reliable detection.
3. There are special stereo cameras like the Bumblebee you can purchase.

Since it seems you are very unfamiliar with stereo vision processing, I recommend read the chapter on stereo vision in Szeliski. You also should more clear on your requirements, are you primarily interested in doing object detection, or 3d reconstruction using stereo cameras? Both of these are active research topics, and they are only partially related to each other, i.e. you can do object detection without using stereo reconstruction.

In response to your questions:

1. If you want to do any sort of geometric reasoning about your scene, then autofocus is absolutely taboo. Auto focus changes the intrinsic camera parameters and thus makes estimating high quality metric scene geometry near impossible, and definitely not real time. The typical workflow with stereo cameras is that they are manually focused and rigidly aligned specifically for the type of scene, calibrated and then unchanged.
2. Autofocus may not have any effect on object recognition depending on your detector type. If it uses only 2d image information, then this will likely have little effect, but if the detector requires 3d information then autofocus will prevent reliable detection.
3. There are special stereo cameras like the Bumblebee you can purchase.

Since it seems you are very unfamiliar with stereo vision processing, I recommend read the chapter on stereo vision in Szeliski. You also should more clear on your requirements, are you primarily interested in doing object detection, or 3d reconstruction using stereo cameras? Both of these are active research topics, and they are only partially related to each other, i.e. you can do object detection without using stereo reconstruction.