If you mean the more conventional phasers that were rarely used, they were animated as coming from somewhere close to the bridge module despite no such emitters being part of the model. IIRC, it was only the one emitter that was used during the fight with the Lakota and not in any other episodes, although my memory might be faulty. 
I do recall that some sources like Starfleet Command 3 suggest the pulse phasers have a trade off for their increased power, because of how the shape of the energy differs. They deal more damage than a conventional beam but at the cost of having less range, somewhat like how the Romulan plasma weaponry tends to be highly destructive but unstable enough that most other races haven't made as much use of it. The Defiant's mobility easily offsets the range problem.

I do recall that some sources like Starfleet Command 3 suggest the pulse phasers have a trade off for their increased power, because of how the shape of the energy differs. They deal more damage than a conventional beam but at the cost of having less range, somewhat like how the Romulan plasma weaponry tends to be highly destructive but unstable enough that most other races haven't made as much use of it. The Defiant's mobility easily offsets the range problem.