The answer to this question really depends on the specific subs that are being compared.
In the case of the Hsu Research products referenced earlier, we would generally recommend a single STF-3/VTF-3 over dual STF-2/VTF-2. For one, the single 12" (meaning, 12" diameter driver) sub is less expensive. Two, when set side by side, the single 12" sub takes up less floor space. Three, it is easier to hook up a single sub. Four, the 12" sub will have lower tune and frequency response than two 10" subs.
Dynamic compression limit of the Hsu 12" subs is significantly higher than the Hsu 10" subs (although the VTF-2 in particular can get quite loud in the common bass frequencies due in part to having dual heavily flared 3" inner diameter ports). Dual Hsu 10" subs are needed to get closer to the dynamic compression limit of the single 12" sub. The larger enclosure on the 12" sub also allows use of longer ports for lower tune, and adding a second 10" sub to another identical 10" sub will not change the basic port length, so it would be advantageous to go for the single larger subwoofer for lower frequency response. However, if floorspace is at a premium, stacked subwoofers with the 10" diameter drivers will naturally take up less floorspace than our subwoofers with 12" diameter drivers. Also, if maximum output at relatively high bass frequencies is desired, it is entirely possible that a combination such as dual VTF-2 have more undistorted clean output at these higher frequencies than, say, a single VTF-3. Finally, if one is looking for low bass for a 2-channel audio system, they may be able to more easily smooth out response using two smaller subwoofers rather than a single larger subwoofer (noting that it is generally more difficult to set up two subs in this configuration).