Does this work for you:
zip -ry archive.zip [0-9]*
Run on a directory containing this:
001 002 100 200 aaa bbb
it creates a zip archive of only the numbered directories:
$ unzip -l archive.zip
Archive: archive.zip
Length Date Time Name
--------- ---------- ----- ----
0 2010-10-19 22:27 001/
0 2010-10-19 22:27 002/
0 2010-10-19 22:41 100/
0 2010-10-19 22:41 100/10000/
0 2010-10-19 22:41 100/10000/a.txt
0 2010-10-19 22:41 100/10000/10000.txt
0 2010-10-19 22:27 200/
--------- -------
0 7 files
That is only numbered files/dirs at the top level get put in the zip archive.
UPDATE
To exclude files from the top level:
find . -maxdepth 1 -type f > excluded.files
review 'excluded.files' carefully. Then:
zip -ry test.zip [0-9]* -x@excluded.files