According to Wikipedia (and my personal understanding), cargo-cult programming is the superstitious inclusion of code that serves no purpose, merely for the sake of conforming to some remembered template. However, as you say in ref($proto) - just say no!:

Rather, I'm saying that "new" on an instance could mean either "clone" or "make new one like...", and thus you are confusing at least half your audience, guaranteed.

Thus you have already described at least two purposes of this construction. The fact that experienced OO programmers don't all agree on which purpose it should serve doesn't make the construct invalid—the idea that the existence of differing possible interpretations means bad code seems (to me) entirely counter to TIMTOWTDI.

Anyway: even if this construction is a bad, or at least inelegant, idea (which I think that it is), I don't think that automatically makes it cargo-cult programming.