The technique I think you are referring to is called "resistively damped operation"...
And generally you don't simply short the 'extra' voice coil, but rather you wire a resistance across it (although you could just short it, but it wouldn't really provide any benefit

).
This isn't EXACTLY your situation by the numbers.. but this example is the same, just a little simplified for other readers, if I am understanding your situation correctly:
Let's say you have a dual 2 ohm sub that handles 1600 watts (800 per coil), and you have an amplifier that makes about 1600 watts into a 1 ohm load.
In this case, simple. You just wire the voice coils in parallel (tie all the +'s together, tie all the -'s together), and end up with a 1 ohm load presented to the amp, which therefore makes 1600 watts through that load. All fine and dandy...
...until the day you decide one sub isn't enough, and you really like your stuff, so you buy another of the same sub. Now, you have a total of four 2 ohm voice coils (two per subwoofer).. you can't wire them to yield a 1 ohm load, period.
But you COULD wire just one voice coil (2 ohms) of one subwoofer in parallel with just one voice coil of the other subwoofer, and end up with the same 1 ohm load that you had previously.. the amp would make 1600 watts, each sub would get 800 watts, all would be fine and dandy... there's just the issue of what to do with the now-vacant coils! //content.invisioncic.com/y282845/emoticons/wink.gif.608e3ea05f1a9f98611af0861652f8fb.gif
There are a couple things to be aware of, but none of them having an impact on the enclosure for the subwoofers... Qes will be higher...
Generally, reaching maximum output on "just" 800 watts wouldn't be an issue too much, as you can go larger on the enclosure, and reach maximum excursion with less power (two legs of Hooke's Iron Law: enclosure size and efficiency are proportional).
Not to mention it takes a quadrupling of power to effect a doubling of excursion (and that's the theory.. in reality, it may be worse!//content.invisioncic.com/y282845/emoticons/wink.gif.608e3ea05f1a9f98611af0861652f8fb.gif).. so you don't have as much ground to make up as you might think.
You could just wire a jumper across the + and - of each vacant coil, and be done with it.
But why do that?
You can have more fun with it than that..
Resistively Damped Operation allows you to actually vary the Qts of the driver, based on the amount of resistance placed across the coil.
The real fun to be had is when you wire a potentiometer across the 'vacant' coil.. then you can turn the dial, and change the Q at will! //content.invisioncic.com/y282845/emoticons/biggrin.gif.d71a5d36fcbab170f2364c9f2e3946cb.gif
Adire has a great article in their tech library about it, I highly recommend you give it a read:
http://www.adireaudio.com/tech_papers/rdo_operation.htm