That is an interesting question, and my "hunch" is that it may be used to avert FX that may react to audio even if it is silence (although none come to mind readily). It also allows for editing to be more discrete (which may be the real reason). Clips also allow for FX to be used on a clip-level rather than in the entire track, which can mitigate CPU-intensive plugs.
From a "disk usage" perspective, a clip is simply a window into the underlying wav file, so it is possible to have a 40GB wav file but only be using 1 MB of it (incredibly extreme example). After I get to a certain point in editing, I will bounce clips to create a new audio file for the simple reason that playing a single wav file is easy (is all Windows Media Player does) and not CPU/disk intensive at all.
From a "big picture" perspective, I think this is more a matter of taste, since machines now have enough RAM/speed that "clips all over" isn't going to cause issues unless it gets "too intense" (like the extreme example above).