cmd files may technically be programs, but people interact with them like text. they're more like modern-day scripts, really.
in
 trying to salvage old files off my working drives (to replace the files
 on the trashed one), i've noticed that i'm often able to pull text 
files up that have been deleted for up to five years but i can't pull 
off cmd files that were deleted last month. it doesn't seem to be 
dependent on size. i'm led to conclude that ntfs is filing cmd files as 
programs and they're getting easily corrupted as binary.
but they're not really programs. they're certainly not binary they're text...
i
 realize that there may be some security issues with treating scripts as
 text files. but how serious an obstacle is this nowadays really? i 
mean, if you can launch notepad remotely, you're pretty much in control,
 are you not? even so, wouldn't it make more sense to block at the 
kernel than the file system? even backup drives crash. rather, this 
strikes me as an ancient windows artifact from the early 90s or the late
 80s when cmd files really were programs and that should be updated for 
modern usage. i can't be the first person that's run into this.
i don't know enough about other file systems to comment.