Sound would not be affected. Sound treatment should occur on the bottom and top of the trusses.

The greater depth would be much stiffer and better avoid a bouncy feeling. Bounce is not always considered in the design of a floor structure so you need to ask the engineer (not the builder) what the maximum deflection at the design load is of each option. A really stiff floor would deflect no more than L/720 (.33 inch).

The openings for ducts would be larger but you need to find out the size of the largest duct needed. The smaller truss should allow at least an 8" round duct and the larger one should allow at least a 10" round duct which is 60% larger. The smaller trusses can sometimes be designed to allow a larger duct at a specific location. If the ducts have not been designed you probably should not be selecting the trusses.

16" spacing makes it much easier to position and install recessed lighting but if you are concerned about sound transmission you might want to limit ceiling penetrations or put them in sound/fire boxes.

What is the downside of the larger trusses?

I also do not think that it will make a lot of difference as far as sound transmission goes. You need to ask the engineer these things.

If cost is not a concern than it is almost always better to have a deeper stiffer floor. (within reason)

If you need sound proofing that could be designed in.