The index.php files in some modules mean that this module has a start page which is not a list page, so adding empty files would just confuse the schema. I'am not a fan of adding unescessary files btw.
. The current situation is not as it should be and fixed in svn already. But it does not really harm on the other hand as all files are written in a way that direct access without logging in first can not be misused and which files are available in a folder can everybody see by downloading the ispconfig tar.gz, so even if the -Indexes would fail on a server, its uncritical.