Suppose the pucks start spinning after the collision, whereas they were not before. Will this affect your momentum conservation results

No, it will not affect the results.

Explanation:

For elastic collisions in an isolated system, when a collision occurs, it means that the systems objects total momentum will be conserved under the condition that there will be no net external forces that act upon the objects.

What that means is that if the pucks start spinning after the collision, we are not told that there was any net external force acting on the puck and thus momentum will be conserved because momentum before collision will be equal to the momentum after the collision.

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