I have an administrative account I use to perform installations. I used that account to install SDE. That account is still a login to the SQL Server, but that account is now just part of the public role, whereas before it was part of sysadmin.
I was thinking that the DBA might have changed what I can see with my login and perhaps the other sql logins I created during the SDE install: sde, gis, gisreader, are all still there.
When I connect from ArcCatalog to SDE, I have three direct connections, one for each user: sde, gis and gisreader. So you must be correct in that those logins are still there, i just can't see them.
sde: connect, create function, create procedure, create table, create view
gis: connect, create procedure, create table
gisreader: connect, permissions granted via ArcCatalog on individual layers, View-Grant.