The email sent on user registration is a text only email. we did this to minimize the chance that the registration emails would be caught in spam filters.
You could update the WA_UniversalEmail/email_templates/registration.php page, and change line 9:
<?php echo($WAGLOBAL_Root_URL); ?>users_Confirm.php?ID=<?php echo(mysql_insert_id()); ?>&code=<?php echo($_SESSION['randomConfirm']); ?>
to:
<a href="<?php echo($WAGLOBAL_Root_URL); ?>users_Confirm.php?ID=<?php echo(mysql_insert_id()); ?>&code=<?php echo($_SESSION['randomConfirm']); ?>"><?php echo($WAGLOBAL_Root_URL); ?>users_Confirm.php?ID=<?php echo(mysql_insert_id()); ?>&code=<?php echo($_SESSION['randomConfirm']); ?></a>
but this increases the likelihood of the email being flagged as spam.