Hi there,
Sure, some have more than one sub. I have three, if you count the two in my Definitive towers. Advantages could include more bass, smoother bass with less effort, stereo subs to maintain front imaging (in which case you wouldn't want to use the two sub outs, you'd want to maintain Left and Right). A large room may not be well serviced by only one sub, so you may need more than one sub to get to "normal" or, if desired, "room-shaking" levels.
That's a start. I bet there are more reasons that someone around here could think up.
Have a great day!
-- Otto