• I'll make an educated guess about compressed files later.
• Most every modern filesystem supports sparse files, and the call underlying -s reports the virtual, not on-disk, size, on most of them. I assume NTFS is no different. Programs have to specifically be "sparse-aware" to deal with such files properly.
• The size of alternative streams is not reported by the call underlying -s. Again, programs need to be "alternate-stream-aware" to deal with this situation correctly.
• It reports the byte size of the file, not the cluster size. Unless you are writing a lowlevel filesystem manipulation/report tool, you shouldn't concern yourself with this distinction in the first place.

You'll notice that the defaults are such that a program naively copying the contents of a file to another with taking the existence of advanced filesystem features into account will still work (and that's on OS level, not Perl -s level). In light of that trend I'd suggest that -s reports the uncompressed size of NTFS compressed files.

And that's probably all the OP needed, too.