Poul Anderson says in one of the Flandry novels that there are a huge number of rogue planets (planets not in a star system). That'd account for some of the missing matter.
Well, Anderson may have made a lucky guess, but at the time he had no was of knowing that, so it doesn't make much sense to cite that as your evidence for the idea.
However, there's no way that would be enough to account for the majority of the missing mass. If it were baryonic matter, there'd be a lot more light extinction from all the clutter in between the stars.
As for making the replicators not work, they're what the Reeves'Stevens' called transtator tech - based on subspace effects, like the shields, warp drive, transporter, etc.
The term "transtator" was introduced, and established as "the basis for every important piece of equipment that we have" (in Spock's words), in the TOS episode "A Piece of the Action" by David P. Harmon and Gene L. Coon.