That'd depend on the definition of "Main Engineering". One could argue that in TNG and TOS, we see only the control room of the vast engineering complex, whereas ST:TMP is the first to show the actual, usually uncrewed mechanisms inside. Only this time, they are crewed, because the recently refitted ship is undergoing testing - but it's not a shirtsleeves environment, as the supposed radsuits testify. In ST2, the facilities are crewed again, because it's a training cruise.
And STXI shows the comparable innards of a TOS era starship in relatively standard conditions, proving that people are normally not to be found in there. All the engineers stay in that small control room we saw in TOS (or in its analogue for this movie).
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).