Sorting by vendor seems to make the most sense to me; that's the easiest what to remember where things are, even if some folders only contain a few entries. Plugs that came in a package go into a common sub-folder.
If you pay attention when installing i.e. install them to separate directories as suggested above, this is sort of automatic. I used to do that, but latelyI create my set-up (still by vendor) in the Cakewalk plug-in manager, because
- I only want 64 bit version to show if both 32 and 64 bit would be available
- I shorten the names for better display on the control surface and FX bin