It does work, but bear in mind that's only if you've directly selected ships.
When you have selected an entire fleet or multiple fleets, there's no way to "divide a fleet in half" in terms of the way the selection works. That's why a variety of deselection things don't work at this point -- those ones are based on deselecting specific ships, etc. But when a fleet is selected, it makes darn sure that all its ships are also selected, by its nature.