> An additional method is to do as you were inquiring about - throw them into one giant folder.  I would never choose to do that myself, but it is your planet.  
 
+1

Throwing all VSTs into one folder can be problematic IF and I say IF a 64 and 32 bit dll is named the same. Believe it of not, some vendors still do that.
 
A sub-folder for 32bit (ONLY) plugs is one way to go and I do that. That sub-folder (for me) is dwindling. I only have two plugs that are wonky in 64bit.

If your x64 and x86 plugin folders do, in fact, have identical contents, remove the x86 folder from the scan path and you're good to go...
If you do find an errant plugin that is x86 only, create a x86-only folder and add that to the scan path.