All Seeing Eye
Admiral
The Borg aren't destroyed.
Admiral Janeway said the thing she infected them with was "just enough to bring chaos to order" and said nothing about it being enough to wipe them out.
We only saw the unicomplex destroyed and after infection we really only saw a communication problem between the Queen and the collective and not much else. She even said herself that a sphere could still hear her thoughts and it appeared to function perfectly fine even with the Queen infected and the communication system malfunctioning.
The shields on the transwarp hub rings were controlled directly by the Queen and the unicomplex (as was mentioned onscreen) and therefore Admiral Janeway only needed to infect the Queen and unicomplex to disrupt her from adapting the shields on the hub rings.
Since we know Borg Queens have died previously (first contact) and we know they must have been seperate queens for obvious temporal reasons then a new Queen no doubt took command of the collective from another complex.
So in Endgame we saw the death of that particular queen and the destruction of that particular complex and we saw only a communication malfunction between the Queen and collective.
So once the unicomplex and queen was destroyed a new Queen would have taken over the collective and order restored to chaos.
Since the queen said they had assimilated the armour technology that means that post endgame the Borg still exist in their full glory and hey have the knowledge for building and defending against the armour technology.
The only thing the Borg suffered was the death of a single queen, the destruction of a unicomplex and the destruction of the Transwarp Hub.
For some reason I had it in my head that in Endgame the Borg were destroyed but I realise now after watching it again on Virgin1 that the Borg are very much still alive.
Since we know the armour and torpedoes were developed specifically to combat the Borg Admiral Janeways actions have got Voyager home but weakened the Federation against the Borg and made the Borg stronger. Her actions have done more harm than good.
Admiral Janeway said the thing she infected them with was "just enough to bring chaos to order" and said nothing about it being enough to wipe them out.
We only saw the unicomplex destroyed and after infection we really only saw a communication problem between the Queen and the collective and not much else. She even said herself that a sphere could still hear her thoughts and it appeared to function perfectly fine even with the Queen infected and the communication system malfunctioning.
The shields on the transwarp hub rings were controlled directly by the Queen and the unicomplex (as was mentioned onscreen) and therefore Admiral Janeway only needed to infect the Queen and unicomplex to disrupt her from adapting the shields on the hub rings.
Since we know Borg Queens have died previously (first contact) and we know they must have been seperate queens for obvious temporal reasons then a new Queen no doubt took command of the collective from another complex.
So in Endgame we saw the death of that particular queen and the destruction of that particular complex and we saw only a communication malfunction between the Queen and collective.
So once the unicomplex and queen was destroyed a new Queen would have taken over the collective and order restored to chaos.
Since the queen said they had assimilated the armour technology that means that post endgame the Borg still exist in their full glory and hey have the knowledge for building and defending against the armour technology.
The only thing the Borg suffered was the death of a single queen, the destruction of a unicomplex and the destruction of the Transwarp Hub.
For some reason I had it in my head that in Endgame the Borg were destroyed but I realise now after watching it again on Virgin1 that the Borg are very much still alive.

Since we know the armour and torpedoes were developed specifically to combat the Borg Admiral Janeways actions have got Voyager home but weakened the Federation against the Borg and made the Borg stronger. Her actions have done more harm than good.