Ductwork above ceilings should have very few vertical transitions; having unnecessary bends and transitions makes the fan work harder and the system becomes less efficient. The cable trays I've seen are always run at an elevation below the ductwork all but eliminating conflicts. Then during construction, the GC will offset small duct branches, piping and your cable trays as needed to make everything fit.
To answer your question, it does not matter.
IF you are that concerned about conflicts, the best thing to do is layout where you want the cable trays then talk to the HVAC designer to coordinate.
Being in a position where I frequently review designs, I cannot tell how how often I've seen plans where it is clear the engineers and architects have not coordinated with each other. It's as if they are each in their own little worlds.