There is one case I know of where Emacs (via Cygwin) has performance issues on Windows: listing directories in remote volumes. Per StackOverflow [0], dired is slow because `df` is slow on NTFS. So, you can eliminate df to speed up dired by a lot.

`(setq directory-free-space-program nil)`

0: https://stackoverflow.com/questions/26128693/emacs-dired-slo...