The login prompt is a funny thing in Hurd, you can actually run commands, cat files, etc :P
Executing reboot will run rc.shutdown and print the corresponding messages as if root were there current user. But finally when /sbin/internal_reboot is run it fails because of insufficient privileges.
At the login some kind of *unnamed* guest user is active so whoami fails and the script continues. Using id reveals that the uid is 2^32 (or (unsigned int) -1). The following patch drops the usage of whoami.
diff --git a/rc.shutdown b/rc.shutdown
index 0a77615..bac471d 100644
--- a/rc.shutdown
+++ b/rc.shutdown
@@ -6,7 +6,7 @@
. /etc/rc.conf
. /etc/rc.d/functions
-if [ `whoami` != "root" ]; then
+if [ `id -u` -ne 0 ]; then
echo "Only superuser can do this"
exit 1
fi
(the diff avobe has an extra leading space on each line)