Yes, all project files are included in the history and thus their real name will be in the history for the project users file. However, the history for that file is only visible by looking outside of Paratext via Mercurial (like TortoiseHg). It is never shown in the Paratext UI in any way.
The only way to completely remove a user is to use Convert Project to remove the traces of the original name. Since Convert Project takes a long time and creates a brand new project, I’ll leave it up to you to decide if it’s worth it.