You can move your plugins any time you want. It won't break old projects - as long as they can still find the plugins.
For Waves, SONAR just as to know where the waves he'll dll is - and this points other all the actual plugins. You can copy the waveshell dll anywhere you want to (from c:\program files (x86)\vst plugins) and it still works fine.
I have all my plugins in one place - c:\vst plugins\64 bit - in various sub folders. Then sonar only has to scan here, the vst3 folder and there's another one for "c:\program files\cakewalk\shared plugins" (or something like that)