The circuit which switches a LED on and off requires some time to from fully on to fully of and vice versa. During this time, the switching circuit has much larger losses than when fully on or off. For that reason, such circuits are typically designed to switch as fast as possible (where, for example, the maximum allowed gate current of a MOSFET could a limiting factor to the maximum speed). And the switching frequency is typically kept as low as possible, to maximize the time full on/off and minimize the amount of "switch time".
Some LEDs can be more efficient when emitting the same brightness via very short bursts of high current vs. a continuous low current. In the high current case, the LEDs get very hot very quickly. The higher temperature causes a better heat transfer away from the LED, and the relatively long "off time" of the LEDs allows it to cool down significantly. This can improve efficiency over the same LED when it's kept at a constant medium temperature.
While the effects can be calculated, it might be much easier to experimentally find out which setup performs better, given a specific environment/design/components.