Had a little time on my hands so came up with a proper fix..
In /etc/e-smith/templates/etc/modules.conf change all references to $conf to $confref :
my $hisax = db_get_prop($confref, 'isdn', 'HisaxOptions') || "";
my $type = db_get_prop($confref, 'isdn', 'Type') || "";
my $protocol = db_get_prop($confref, 'isdn', 'Protocol') || "";
Then expand the template:
/sbin/e-smith/expand-template /etc/modules.conf