Not adding the clan letter (i.e. Y'shtola vs. Shtola) is a sign of having a deep relationship with the Miqo'te in question.
Only Y'mhitra and Matoya refer to Y'shtola without her clan letter; both of them have very close relationships with her. I can't recall who referred to F'lhaminn without her clan letter, but if I were to wager a guess it would be Minfilia, to whom F'lhaminn was essentially a surrogate mother.