Personally, I like to think of the nacelles and their warp coils as a fairly direct analogy to the propellers of a waterborne vessel. They don't provide any power, they just convert it into motion - and if more power is to be channeled, then one can choose more propellers, bigger propellers, or faster propellers. Just as with nautical technology, each of those choices comes with a penalty, and is only optimal for a certain application range (say, only certain speeds, or certain loads, or certain mission lengths before the parts wear down).
Two is the lowest possible number for differential control of motion (although in three dimensions, it should be three - but perhaps these "props" can also provide differential in "torque"?). A four-propeller beast is rare nowadays, thanks to improvements in building individual props. A single-propeller vessel is rare as well in military use, because redundancy is often worth the extra price of the second prop. The very same reasons might drive Starfleet design: the Constellation has more power than the Constitution refit, but does not yet enjoy the sort of advanced nacelles that could work in combinations of just two, and the Saladin sacrifices the second "prop" because Starfleet can then afford more of these fighting vessels to be used as cannon fodder against Klingons. And the Intrepid may well have "high speed propellers" that are great for sprinting but give abysmal mileage and require frequent cool-down and maintenance, thus being no faster in "per year" terms than competing designs even if they are superior in "per hour" terms.
Timo Saloniemi