Depends on what you are trying to accomplish. If you only run one audio application or all your applications can use the same plug-ins then one big directory tree may work for you. However, moving things around is probably not going to help get a complete scan. Neither is turning off autoscan.
When I had trouble getting a complete scan, I would incrementally build up my scan path by adding one path at a time to the scan path definition in Preferences. If the directory tree could not scan to completion, I would move parts of it until it would scan completely. Then add back pieces, scanning with every addition.
Do not have the same path more than once Preferences. IOW, if your scan path include "C:\Program Files\Cakewalk\Vstplugins," do not add any children of the path and do remove any which already exist. For example, if the path also contains "C:\Program Files\Cakewalk\Vstplugins\Cakewalk Sound Center," remove it. It is redundant and can cause problems.
It is not a particularly good idea to mix 32bit and 64bit plug-ins in the same path especially if they are the same effect. In 64bit installations, Cakewalk does install some 32bit plug-ins in 64bit directory tree. My guess is to reduce the scan path and installation as simple as possible. I avoid adding third party 32bit plug-ins to the 64bit path.