In DNN 5, if you delete a portal, its users will show up in Host:: SuperUser Accounts. However, no reason to worry, hose users are not granted superuser privileges nor do they have access to any other portal in your DotNetNuke installation; the cause for them to show up is the superuser module, which shows all user records, which have no associated record in userportals table, like superusers. Starting with soft-delete users, if removing a portal, user records are not touched and those leftovers show up as Superusers and prevent re-using the usernames.
To fix this situation, you may run the following script from inside Host :: SQL:
DELETE
FROM {databaseOwner}{objectQualifier}users
WHERE userID NOT IN (SELECT userID from {databaseOwner}{objectQualifier}UserPortals)
AND IsSuperuser = 0
DELETE
FROM aspnet_membership
WHERE UserID NOT IN (SELECT A.UserID
FROM aspnet_users A
INNER JOIN {databaseOwner}{objectQualifier}Users U
ON A.UserName = U.UserName)
DELETE
FROM aspnet_users
WHERE UserName NOT IN (SELECT UserName
FROM {databaseOwner}{objectQualifier}Users)
(tested with DotNetNuke version 5.3.1)