Trying to guess the structure of a wiki in advance won't work. A wiki will evolve into the optimal organization of information as people use it, and it's better to adjust the structure based on the content, instead of the other way around.
If there are lots of empty pages in your wiki, and people are putting content elsewhere than those pages, then the wiki is probably subdivided too much.
“It's best to start with as little structure as possible and only add more structure when it proves to be needed.” - Ken Tyler, Seedwiki
If you see pages that are empty, and content of the same topic as those empty pages being developed elsewhere, let the content continue to grow and delete the empty pages.
Once content grows to a point that it should be separated from the core and given its own set of pages, propose this to the community by leaving a comment on the page containing the content.