I always think this joke is more of a linguistics/grammar joke than programming. The kid resolves the ambiguity in the ellipsis incorrectly, but why is this a programmer joke?
For a serious reoly, I think the expression "If they have eggs, buy two" is redundant. If they didn't have eggs, the kid just can't and won't buy any eggs.
I think the proper command would be, "Please buy 1 bottle of milk and two eggs." That way, the kid won't be confused and it's still a proper valid command.
Unfortunately though, the sentence is ambiguous even to non-programmers. It is unknown whether the if condition applies to
buying two eggs (buy two eggs)
buying two bottles of milk (buy two bottles instead)