I think the big difference between the numbered novels and the current books since the DS9 relaunch is that there has been a concentrated effort on the part of the Editor overseeing the Star Trek line to create both large stories that spanned multiple novels, and smaller stories that still had interconnected pieces between the novels. It's been a collaborative effort between the authors (again supported by the Editor of the trek line) to carry over details of plot and character growth between each other's work.
Well, there hasn't been just one editor in that time. Marco Palmieri may have done the most to establish the modern continuity, but he did so in collaboration with others including John Ordover, Keith R.A. DeCandido, Margaret Clark, Ed Schlesinger, and Jaime Costas. And of those, only Ed and Margaret are still involved with Trek editing.