It could also do with her shuriken only... afterall to some adults many teens look similar(not that I am saying vincent is shallow)... but vincent may have seen her shuriken... perhaps it is a weapon that is ancestrial in Wutai, and perhaps it is only used by female warriors. etc.

Perhaps the shuriken was Yuffie's mothers and Vincent had seen or know her mother when her mother was young, this I believe is the most likely although many possibilities spring to mind.