You're actually reading and testing every entry in your
directory, which probably accounts for your "disk activity".
Directories with more entries will obviously take longer
than others, especially heavilly loaded ones. There is
no built in "filter" for readdir, to the best of my knowledge,
so finding directories with subdirectories is going to be
involved, even in the best circumstances.
Your second solution just reads in everything and then
backtracks to find subdirs. If this is faster, then a
native implementation of the "dir /ad /b" command might
help you out.
If you query in an overlapping way, such that you are
actually testing the same directory twice, caching your
findings in a hash may save you the trouble of the test.
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