...oddly a hard restart solved it. This is the second time this has happened since iOS10.
Also, it is weird how some numbers show the name, and a few only the phone number.
I was able to fix this on my phone and my wife's. the issue was multiple accounts being synced to the phone that had the same contact in them. I was able to minimize both our phones down to one contact list and everything works fine.
Either no contact card (obviously) or duplicate contacts will cause that. If the iMessage ID is an email and you have that email on two contact cards it will show the email address, same with phone number.
...thanks for the responses. I'll confirm, but, I only have one email account on my device, and only one Contact card for said Contact(s) with the issue Albeit, I'll check again.
I was able to fix it by editing the contact numbers to remove the 1 at the beginning (assuming you're in U.S.). For some reason most of my contact had the 1 added when I update to iOS 10. Whenever I add contacts I always start with area code and skip the 1.