Looking over the list of family names, nothing really stands out to me, but my inclination is to assume they have a variety of origins: place names, occupations, references to Saisio history or mythology. I'm by no means an expert on Caldari, but they seem to hold the family unit as highly important and do not seem overtly chauvinistic (many Mega CEOs are female, as well as military officers, etc). Also there is some emphasis on achievement and personal contribution to the whole. As such, I do not believe it out of place for a family name to descend from whichever parent has the 'dominant reputation', but that is of course but one option.
Regarding the Minmatar, I tend to defer to the players' clan law and family dynamics. For instance, often times Vherokior clans are matrilineal so I play and write them as gynocentric, for lack of a better term.