It destroyed the Queen and the Hive Mind as well as trashing their galactic Transwarp network which was the backbone of their empire. As we saw in Voyager's "Unity" episode though, Drones can easily create new Hive Minds as well. So I'd imagine they would be in a situation similar to how the Zerg have been in StarCraft when left without a central leader.
Star Trek Voyager was terrible when it came to Time Travel, ie. they relied upon it far far too frequently. They even made a running joke about how Janeway made it a point in life to avoid "temporal issues' but would still far too often be the victim of many, or in the finale, just make them herself.
I wonder if Voyager had the most time travel episodes out of the whole series?
The queen has been killed 3 times now, so I doubt that was the end of her. Everything else can be rebuilt easily enough.