Depends what you mean by thermals, the dual chip card doesn't double up as much on components as two cards and so adds less heat to the case due to lower power draw. But if you're watercooling anyway it's mainly space constraints of two cards you would be concerned with.
Dual cards tend to add more heat to the case as they don't normally use a classic blower like those found on single cards. Half the heat goes out of the back of the card and the other half goes into the case.