Let's do some physics again:
All culinary aspects aside, a roast is a (more or less) solid "blob" with a certain mass and volume.
To get the roast to the desired doneness, you want to reach a certain temperature at the center of the meat. The crucial properties are the thermal conductivity and thermal diffusivity of your meat or, very simply put, how fast your meat transports the oven heat towards the center of your roast, which again is calculated on oven heat and starting temperature of your meat.
This depends on geometry, or, the maximum thickness of your meat. Hence the rule to stick your meat thermometer in the thickest part of your meat.
Two ducks next to each other are two separate masses, which heat up independently, not one roast of greater thickness:
Two ducks in your oven need basically the same time as one duck of the same size.
(A good oven should be capable of heating enough that the second duck won't lower the temperature significantly.)
Now to the practical points:
For the reasons discussed above, it is easiest if you choose two ducks of about the same size and weight. If not, one will need less time than the other and you might have to take one bird out of the oven sooner. If both shall be done at the same time, the smaller one needs to go in a short while after the bigger one - how much time difference is very hard to say, even with those handy "roasting time by weight" charts in cookbooks or on the Internet: Use a thermometer, not a timer, to determine doneness. (And don't forget that the core temperature will rise a few degrees even after you have taken the bird out.)
You ask about positioning in a conventional oven:
By all means roast your birds side by side, not one above the other. Stacked, they will be very close to the top or bottom heating element, which will at least dry them out but more likely burn the top or bottom, while shielding the other bird from the heat on one side. Even if you switch positions occasionally (do you really want to juggle hot pans?), you get the same effect of a "burned-but-undercooked" bird. And no, foil will not prevent this.
And just because we repeat it again and again:
Do not determine the doneness of your roast by a watch, use a meat thermometer.