The "leading edge," so to speak, of the beam is most efficient in a lot of cases. Hence the development of a pulsed phaser cannon, as used in Defiant.
It's almost nothing but.
The TNG Technical Manual also suggests that rapid firing at different sections of an enemy shield bubble can weaken it, so sometimes they are trying to erode the protection overall instead of poke through it one beam at a time, if you follow me.
In other cases, continuous dwell time on the target is the most effective approach. The choice is presumably made by the Chief Tactical Officer and depends on the type of target and the goal of firing phasers at it, and it is one of many choices that must be made about the phasers, including power level, frequency and nutation.
The Tech Manual suggests the continuous firing time of those arrays is measured in minutes, so the heat issue isn't likely to come up too often, but the issues of power consumption and of intentionally limiting damage to certain targets are more prominent.