We have used both in my past LMS lives...As long as you have a value that is unique and stable you should have no issues...in fact your unique employee ID might be better than email since that could change in some cases (change to married name, same names, emails can sometimes be re-used after a period of time, etc.)

I’ve done this. Make sure you choose a value that is NOT going to change. As @lrnlab pointed out, emails do change. We’ve ended up using our internal object Id for our users as our usernames changed just like emails when people got married etc.

It’s not ideal as it does show up in some places where I would prefer a human readable name, but so far I can work with it. This is most notable on the “Reports” tab of a course, you only see the ID’s, but you can search by name too, so it’s not awful. At least we don’t end up with duplicate accounts anymore.

Make sure you export your users to CSV first, and preferably test the change in your sandbox before committing to it in live. It was a straightforward swap for us though, we went from using email to object ID.

Lovely, thanks Maz.  I had not considered the Reports tab, but as you say a search by name is still possible.