On the issue of who or how many died, one might argue that virtually nobody did. The starship is a pretty safe place to live in, and all the filaments did was shut down systems that provided access. There were probably dozens of layers of backups for things like life support - and procedures that called for people to stay put and wait for rescue.
Exploding consoles are always a hazard, so perhaps a dozen dead. OTOH, whenever somebody dies of an exploding console on the bridge, we don't learn that there would be corresponding deaths on the lower decks. Perhaps the bridge consoles are unique in this respect?
The lack of people on Main Engineering is a bit unusual, though. Whenever we go there, at least some people are messing around - unless our heroes specifically appropriate the space for something silly (such as converting it to a gun range in "Mind's Eye") and supposedly order everybody else out. So perhaps the filaments did hit Main Engineering relatively severely, killing many (and disposing of their bodies somehow).
Well, Riker did say to prepare Ten Forward to receive wounded and casualties or something like that. It was heavily implied that the ship was severely damaged and lots of people were dead and injured. People complain about reset buttons between
episodes of Voyager, but what about that HUGE reset button during
that TNG episode there? That's what really bothers me, I hate the way that episode ends. I really like the episode up until that point. But that ending...