Which ISPConfig version do you use? When I delete a shell user on a ispconfig 220.127.116.11 server, then it gets removed correctly and I can reuse the same shell user name.
Thus, creating a new shell-user in ISPConfig 3, re-using the old name does not change the ID.
web1 id 5009
shelluserweb1 id 5008
Thats the intended behaviour. All shellusers of a website share the same ID, otherwise the shell user wont be able to edit any files of the website.
I guess your problem might be that webmin is not showing ispconfig shell users correctly. If you like to know if a shell user has been deleted, take look in the shell user list in isponfig and dont use webmin.