"Smith" and "Jones" are family names, not given names, at least usually; they can belong as easily to women as to men, and I would guess have belonged to women and men in roughly equal proportion in actually existing life. However in philosophical examples it seems that by far the majority of Smiths and Joneses have been men, or at least male. There presumably exists no high-minded justification for this practice, such as Velleman offers here and there for using "he" and friends as gender-neutral third-person pronouns and adjectives. We could come up with some low-minded explanations, though:
1. Philosophical examples take place in a world quite like our own, except with stricter rules regarding the disposition of surnames; in particular, the initial population of Smiths and Joneses in this world was all male, women keep their surnames on marriage, and no Smith or Jones has ever had a daughter (or perhaps daughters inherit the surnames of their mothers and sons of their fathers). Examples which concern naming customs, of which I'm sure there must be some, are governed by extremely complicated rules.
2. The Smith referred to in these examples isn't a cipher at all, but rather Michael Smith. What began as a joking practice in some seminar ("suppose", says one student, "that Smith here did such and such. Then obviously ...") took off and has propagated throughout the philosophical community, to the point that most people have no idea about whom they're really making these sometimes quite scurrilous suggestions. Jones is Indiana Jones, or maybe Sellars' Jones, who proved himself so useful when he first appeared and who has therefore been recruited by other ambitious philosophers somewhat in the fashion of whichever of the characters in At Swim-Two-Birds it is who does this.
3. It is a reflection of the assumption that arbitrary or anonymous ("Smith" at least being famously not very specific) persons are male.
4. "Smith" and "Jones" are actually given names in these examples. While they are relatively uncommon as given names in actually existing life, we do know that in some societies there exists the practice of giving a son his mother's maiden name as his first name (or middle name, but one can certainly go by one's middle name); I believe that (William) Robertson Davies was named in this fashion, and that his character (Percy) Boyd (later Boy) Staunton was as well. So it's certainly possible that these people are named, say, Carol Smith Fitzwilliam or Jones P. Cooper.