Why will chmod 0000 directory-name not clear the special bits on the directory?

Solution 1:

0000 was considered ambiguous, since it might just mean 000, plus a leading zero since it's octal.

http://lists.gnu.org/archive/html/bug-coreutils/2011-03/msg00162.html

0755 is not explicit - it is ambiguous with people that are explicitly using printf %#3o to output a 3-digit octal string with leading 0 - I don't think we can change this.

That coreutils discussion thread starts with someone quoting the chmod man page noting this limitation:

you can set (but not clear) the bits with a numeric mode.