A heavier wheel figures into
A heavier wheel figures into the equation twice. First, there's the actual weight addition, just like adding water bottles or anything else.
Then there's the rotating intertia. Wheels have to be accelerated, and adding weight to the wheels adds rotating intertia, increasing the energy required to accelerate the wheels, and thus the bike. Think of adding weight to a flywheel.
That's why you don't see deep rim wheels on climbing bikes in UCI races.
This is true and in races where seconds matter over a hundred miles, this will be an effect. For things like RAAM where you have days where you are just climbing and not decending, reducing the mass makes sense too.
But for most of us, most of the time, the mass isn't that big of a deal. At worst, you can count the mass of the wheel twice as far as accelerating goes (but not for climbing) and this assumes that the mass of the wheel is entirely at the outer edge (which it isn't).
If you're a professional racer, worrying about weight makes sense. If you're an overweight slob (like, well, me) then you're better off worring about the 10 extra lbs your carrying around your mid-section and don't worry about the weight on your bike. If you're somewhere in between, then pop some numbers into Excel and see where you are.