The single prop should be more efficient if both systems are designed properly. My understanding is that the benefit of a twin on UAVs is ease of mounting the payload (counter-rotating props is nice too).
Note that one larger propeller is more aerodynamically efficient than two smaller ones totaling the same area. That is a big drawback in efficiency for using two electric motors instead of one.
From the RPM-efficiency curves I have seen for DC motors, and from what I have read, the efficiency tends to peak at right around 1/7th the no-load RPM while the power peaks at 50% no-load RPM. Better to load it a bit too much and have it run a bit slower than load it a bit too little and have it run faster since the slope on the side that is underloaded drops off much faster than the slope on the side that is overloaded.
If you want to get peak efficiency when it occurs at such a high RPM combined with the efficiency of large propeller, you will probably need a gearbox. Gearboxes are expensive so you probably don't want two of those.
If the mission profile allows, you might benefit from designing the motor-prop for maximum efficiency during a climb and then operate it to repeatedly climb and descend in an unpowered glide rather than design it for maximum efficiency in cruise and then cruise under power the entire time.
A motor-prop combo designed to be most efficient during cruise will produce just enough thrust to overcome the drag so that it can be running the entire time with no efficiency penalty, but such a combination will probably have a lot of trouble getting off the ground.
Designing things for optimal efficiency during climb and then operating like a sailplane lets you use a motor-prop combo that is better suited for takeoff while also enabling you to only ever run it at the point of optimal efficiency during travel.