Can a SMPS be turned off to increase overall efficiency for low power applications?
Most low-power-conscious power supplies have power-saving features included, similar to what you have described. There are some considerations to keep in mind.

All switching power supplies have a finite start-up time. The power rails need to be steady, reference voltages need to establish and stabilize, and the switching converter needs to ramp (or soft-start) in order to avoid large stresses on the powertrain elements. A total turn-off usually means a recovery time of hundreds of milliseconds, which could be bad if there's a sudden surge in the load. (In your case, not so much, but power IC designers need to consider all possibilities).

Another method is to keep the controller alive, but simply stop operating the powertrain. The controller will still consume power but there is a net savings as the powertrain devices are not switching all the time.


Pulse-skipping: the setpoint remains fixed and the controller occasionally misses pulses (less output ripple, but possibly noisier)
Hysteretic control - the controller deliberately nudges the setpoint up and down so that the pulses come in smooth bunches instead of spurious skips (the voltage will slew up and down in a sawtooth pattern)


All basic PWM controllers will pulse-skip by nature of the control algorithm (PWM width proportional to the error voltage: if error voltage > reference voltage, PWM = 0%). So this isn't so much a power-saving feature, rather how the controller inherently behaves at light loads. Hysteretic regulation is closer to the spirit of your idea - let the output sag a little to the lower threshold, then send some pulses to recover to the slightly higher threshold. 

In both of these cases, because the controller remains active, there is a faster recovery if there is some input disturbance or load step.

Keeping the pulses more regular results in a smoother output, which your load would likely appreciate. Also, when there is a lot of capacitance on the output, keeping the pulses regular also avoids a large inrush of current being drawn when the capacitor is depleted and needs to be recharged, which is good for component stress and for EMI.