I don't think the connection matters terribly. If you call your child by a nickname, that's what you call them. Johns go by Jack all the time, Richards used to go by *** etc etc Unless you are trying to avoid the nickname, in which case I think more people would call the girl Em/Emmy/Emma etc.
I do think that Emmeline will be pronounced with the long i sound and Emmalynn (as if Emma is the first name and Lynn is the middle name) will be pronounced with the short i sound, so I'd go based on which you prefer there.