My fanwank for why Excalibur lost its entire crew without the ship going kablooey in "The Ultimate Computer" was that M5 got a lucky hit on life support. (always a danger in one of the two board games I played. Maybe the ones with the cutouts and string.) Or intertial dampeners went offline and they turned to jelly.
Related to the spirit of this thread, anyone notice that early in TNGs run...they seem to imply that weapons have far outstripped shield capabilities? See: The Defector
"You still will not survive our attack"
"and you will not survive ours"
Seems like there were a couple of others I'm not remembering that seemed to imply that starships can only survive a couple of volleys.