My interpretation differs from the notion that Janeway completely obliterated the transwarp network, but it's definite that significant and game changing damage was inflicted upon it. In regards to the neurolytic virus and it’s effects on the Collective after the results of Endgame, the term "decimate" historically signifies a reduction of 1/10th in efficacy or capacity, rather than reducing something to 1/10th. Therefore, if the Borg Collective truly suffered a decimation, they would have been functioning at 90% of their previous capabilities, not reduced to 10%.
Seven clearly stated at the end of VOY (in Endgame Part II):
"The Transwarp network has been obliterated Captain".
That's a rather encompassingly finite statement.
Of course, the Borg aren't completely reliant on the hubs to use Transwarp. Remember that they can generate/use their own independent conduits with TW coils... but it seems that there's a drawback to this as it might be power intensive and can burn out the TW coils unless you have enough of them to work in unison (the one TW coil VOY used was able to allow the ship to travel through 20 000 Ly's before it burned out).
Its possible this is why the Borg have built the TW hubs... to make TW travel more efficient. Why having to initiate TW twice, if you can only do so 50% of the time or less for example?
And when the Neurolythic pathogen hit them, the hubs were obliterated (preventing the Borg from travelling with the hubs) and having to rely on their own TW coils - but in a weakened condition and without nanoprobes, they'd have a hard time doing anything and would be easy targets.
If the Neurolytic virus did indeed affect the entire remaining Borg Collective in this way, then it seems as though the Collective has effectively been made ‘sterile’ or ‘neutered’ through the rendering of nano probes as ineffective. However, it raises the question as to why the Artifact was not similarly affected by the neurolytic virus, as this ship appeared to be functioning normally before its sub matrix collapse as a result of experiencing the Admonition.
We don't know what condition the Artifact was in when it encountered the Admonitiob. It was probably severely damaged as a result of the pathogen already and the Romulans were assimilated as an attempt to get some sense of function back... but this ended up backfiring on them and the AI signal/message effectively shut down the artifact.
I also think that the cube in Prodigy’s Let Sleeping Borg Lie was pretty much unscathed from the neurolytic virus once reactivated, Borg nano probes may not have been mentioned in order not to scare or confuse kids too much? Just because something is not mentioned though, it does not mean that it is not there.
No, Janeway DID mention the nanoprobes were non functional in this episode... hence losing the ability to assimilate via these means.
As for the state of the cube... well, that particular vessel could have had its own internal collective on the cube which was in its 'sleeping state' after the pathogen hit. A self-preservation mechanism if you will... so that cube might not have been connected to the Hive in general.
**EDIT**
The Borg Diamond ship at the end of Endgame had adapted to the neuroleptic virus, btw. I just remembered. I think that it wanted to assimilate Voyager… with nano probes.
We have no solid onscreen clarification about all of this really, perhaps we will find out one day in a spin-off or streaming movie.
No, the Borg Sphere (not a Diamond) in Endgame never adapted to the virus (it adapted to the Armor technology VOY had) and was still able to hear the Queen's thoughts at the end of Endgame... the pathogen was likely affecting the whole collective but it took time for it to proliferate across large distances.
My guess is that vessels that were further away from the Queen and the Unicomplex ended up disconnected from the main hive as a result, but this also made them weaker, damaged their nanoprobes, and most ships went into sleep mode... while some got destroyed (I would imagine a lot were destroyed) and only a few ships made it out in severely damaged state which prompted them to go to sleep in an attempt to repair themselves - but with lack of the Hive, they couldn't).