I do not see anything in the default accounts database settings that would be setting "Indexes" to disabled (/etc/e-smith/db/accounts/defaults/)
And it looks like the default setting in the relevent template fragment for httpd.conf defaults to 'enabled' if there is no entry in the database (/etc/e-smith/templates/etc/httpd/conf/httpd.conf/90e-smithAccess40ibays)
simply changing the default might cause problems for existing servers that depend on the current behavior (it's pretty frustrating when a simple 'yum update' breaks something that has been working, as I suspect you know...)
I don't know if there's a way to set a default value of 'Indexes' for new ibays, or for all ibays on new servers. If we could do that we wouldn't need to make any changes to /etc/e-smith/templates/etc/httpd/conf/httpd.conf/90e-smithAccess40ibays, so there would be less chance of breaking anyone's running server.