When you use MC or the OS, i.e Win Explorer or Mac Finder, every time you rename, move or copy files and/or folders, the relationship between individual files and their MC Thumbnails get's broken.
In addition when you use Win Explorer or Mac Finder they will always be quicker than MC at listing folders and the files they contain because they invariably use a File Allocation Table; whilst MC has to check to see if every Folder and the Files within each Folder is/are present, it's building a list of "missing files" every time it is asked to list Folders and Files. Plus, if it's the 1st time it's accessed an individual folder it is probably rebuilding the thumbnails for those files in the background.
When it comes to Moving, Renaming and Copying Files and or Folders, regardless of the number of files involved, after having updated any relevant database/library fields/tags MC hands the task of Moving, Renaming or Copying of those Folders and Files over to the OS; something that is more obvious in Windows than on the Mac.
The decision about using MC or the OS to carry out a R, M & C operation should be based on the Risk Involved and not the Volume/Number of Folders and Files.
If ,for whatever reason, power is removed from the PC while MC is being used to carry out the task you are in danger of having a library/database that is WRONGLY telling you all the folders and files were copied to their "new location" and the only way you can get the folders and files that were not moved, renamed or copied into their "new location" is by using the OS and hope that when you re-open MC there are no missing or damaged/incomplete, files.
MC's R, M & C is a very useful tool but, unfortunately, it contains one major flaw - it updates the library/database Before renaming, moving or copying folders and/or files and not After it's done the task it was given.