From my experience the microwave takes longer to heat two bowls of soup than to heat just one.
But it's not so obvious to me why this should be the case.
Each bowl of soup is a single thermally isolated system, and the same power radiates across each one, so it should take the same amount of time to heat both, no?
Edit: I'm not convinced by the below answers. The answer should depend on the specific mechanism by which a microwave works, because if we ask the same question for a stove instead of a microwave, I would guess that two soups placed on a stove top would take the same amount of time as one soup, as long as the soup bowls have the same geometry and thermal conductivity.