This is a pretty complicated fluid dynamics question, but I'll do my best to make some guesses. In general, I'd have to guess that a whirlpool-waterspout interaction would not do much. Waterspouts are driven by forces in the air, and whirlpools are driven by forces in the water. The actual point of contact might be pretty interesting, but would a waterspout and opposing whirlpool cancel each other? I'd have to say no. Neither could a complimentary whirlpool-waterspout pair amplify itself.
Again, a waterspout is a fairly weak result of powerful atmospheric forces, and a whirlpool is similarly weak when compared to the oceanic forces that cause it. To cancel a whirlpool or waterspout would be to cancel the tremendous forces that bring them to be. Given that these atmospheric and oceanic forces aren't really directly interacting, I doubt they'd affect each other much.