Yes, for every technology there has to be a counter technology (or fix) in order for the show plot to work, because complete, utter, domination would make for boring shows.
What would happen if one race, say the Q, snapped thier fingers and dominated all? Boring. Which is why even Q is made impotent and constrained by other Q, and other too-powerfull beings are above petty human affairs.
Which is precicely why I like the older Star Trek more than the new stuff as visual techno-razzle-dazzle wasn't a big focus and much more was left to the imagination. Also, in Star Wars (episodes 4,5,6) and in Babylon 5 the plot quality gets me watching: the techno-aspects serve merely as background fabric. The new Star Trek shows rely too much on techno special effects to prop up the plot lines.
However, I still think that simultaneous, or even repetative, pin point placement of a crapload of torpedoes right at a single strategic shield barrier point would be both devestating and plausible, even if one's own shields had to be passed on the way out. And it might take preparation time to deliver to target, but it would appear instantaneously to the enemy, leaving no time to evade or counter.
Hey, if I couldn't rip the plot or the techno-physics/science I wouldn't enjoy the shows nearly as much