he says that was the last place that he logged on to the apple id with. i though it sounded a little fishy.
I think your ex-employee can recover his Apple ID by other means...it might take him a phone call, but if he ever used his Apple ID, say for the Mac App Store or iTunes or to purchase equipment, then Apple has his credit card and billing information on file. He should be able to recover his Apple ID from Apple by verifying this information, not by giving the SN of your server, supposedly the last machine that he used his Apple ID on.
Once again, why is his Apple ID tied to your server? Was he purchasing equipment/software with his Apple ID? Was he setting up iCloud with his Apple ID? Any of these reasons you would probably want to correct --- say he setup your server's iCloud account using his Apple ID, then if he recovers his Apple ID he will have full access to your iCloud, meaning all files, multimedia, documents, contacts, calendar events, e-mail, that get automatically "stored" in the iCloud. Personally, I would worry about this if I were you.
I take it that he was not a family member and that he left on what perhaps might be described as slightly unfriendly terms. Be careful!
Regards,
Switon