And we saw later on, that something of a similar line of thought (the individuality meme) DID infect Hugh's ship and all it did was incapacitate their one ship NOT the Collective as a whole.
Hell, are we to assume that Data put the entire Collective to "sleep" in BOBW or just that one Cube? Because both it and Hugh's vessel would be "linked" to the Collective in the same way.
It was clearly just that one ship, Data puts them into the low-power repair cycle. And then the ship conveniently blows up...