The combos don't seem to do anything.
Viewing post in Incremental Pachinko Heaven comments
Combos currently only affect the green zone. Each time the ball passes through a green zone, you earn medals equal to your current combo count.
For example, at the first, a 3-combo gives you +1 → +2 → +3 medals, for a total of 6 medals. If you unlock the +100% node, this becomes +2 → +4 → +6, for a total of 12 medals.