Killing the first one probably won’t any more than killing a single mouse doesn’t stop an infestation, but once the mice realize that you got a couple of cats they will find the exit.
That’s why you need to put traps by the exit too, the mice know too much and might potentially regroup to return with better tactics. You’ve got to get them all in one swift purge.
If the cube is wiped in a single shot, there might not be enough borg left with enough data to adapt. They aren’t adapting magically, they are able to analyze the shot and adjust their shields to block shots.
Ill bet, if they could sneak up on some cubes they could pop a few before the Borg really got wise.