The jury is still out on this one, unfortunately. Let me say for the record though that a soup without veggies doesn't sound too enticing.
Studies have shown that certain nutrients are more easily absorbed by the gut after they've been cooked. An example of this is lycopene, the antioxidant in tomatoes.
Other work has shown that some nutrients, including folate, are destroyed with heat and therefore lost.
Given the fact that it seems some nutrients are absorbed more easily with cooking while others are lost, aim for a healthy mix of vegetables in your next soup. The bottom line is that a daily intake of at least five servings of vegetables, in either cooked or raw form, is important.