16 years old, a young man , when Emma was born. She would naturally have called him formally by the term "Mr" because of that age gap,IMO.

Being the child of an older parent, I consider Emma inclines towards keeping old-fashioned courtesies , and has a similar nature to Mr Woodhouse-she dislikes change as much almost as he- and that, with the above info is in my opinion why she has never called Mr Knightley by his Christian name.

The sixteen year age gap between them also explains why he calls her "Emma",IMO ;-)