Basically the scope of workspace(s) is divided in two points.
First point (and primary) is the eclipse it self and is related with the settings and metadata configurations (plugin ctr). Each time you create a project, eclipse collects all the configurations and stores them on that workspace and if somehow in the same workspace a conflicting project is present you might loose some functionality or even stability of eclipse it self.
And second (secondary) the point of development strategy one can adopt. Once the primary scope is met (and mastered) and there's need for further adjustments regarding project relations (as libraries, perspectives ctr) then initiate separate workspace(s) could be appropriate based on development habits or possible language/frameworks "behaviors". DLTK for examples is a beast that should be contained in a separate cage. Lots of complains at forums for it stopped working (properly or not at all) and suggested solution was to clean the settings of the equivalent plugin from the current workspace.
Personally, I found myself lean more to language distinction when it comes to separate workspaces which is relevant to known issues that comes with the current state of the plugins are used. Preferably I keep them in the minimum numbers as this is leads to less frustration when the projects are become... plenty and version control is not the only version you keep your projects. Finally, loading speed and performance is an issue that might come up if lots of (unnecessary) plugins are loaded due to presents of irrelevant projects. Bottom line; there is no one solution to every one, no master blue print that solves the issue. It's something that grows with experience, Less is more though!