I work at a dance studio and have seen a lot of Sophia/Sofia/Sophies come trhough recently and only one of them ever had a nickname (
Sofia who went by
Fifi). They sometimes get call just "Soph" but only as an occational pet name. So I wouldn't really worry about
Sophia being shortened. It is not something with a set series of nicknames, nor is it a mouthful to say or write. Naming her
Sophia and then just leaving off the "a" every once and a while is certainly an option; but if she is just going to be
Sophie most of the time I don't see the point of even having
Sophia on the birth certificate since
Sophie is a perfectly beautiful name on its own.