Not sure I am seeing the whole picture here.
-First off, having "dozens" of modules floating around as space junk seems like piss-poor planning somewhere, or an episode of the Space Hillbillies. It just sounds wrong. And lazy.
-If they are all captured, then doesn't that imply that someone else is aboard?
-Is the term "module" being used correctly here? Are we talking about living quarters, cargo bays and harvesters? (I guess I get harvesters)
-And lastly, I know this is a zombie-badguy-death-kill game, but isn't the idea of killing your own civilian crews for the sake of "game expediency" a bit much? I, for one, would want such a callous individual put on the GBI's Most Wanted Terrorists list, and have him banned from any planets and star bases operating on the civil side of galactic society.
Just sayin'...