I don't understand what "Do de Rubber Duck" is even doing in a Chanukah episode.
I doubt there's enough footage on the American show that really makes sense in that context. Plus, it doesn't seem like that's ever been a big concern. The American skits that were dubbed are basically there to say "Hey! Our culture isn't completely different from yours because we use the same footage, but dub it in another language" or "This is what our characters sound like in another language."
But the strange thing is, from what I've heard, Chanukah isn't quite the big deal in Israel as it is here, since the holiday is escalated to compete with Christmas. It almost seems, like all Chanukah specials, basically there to explain what it is to Christians. It's a shame that they didn't make a Rosh Hoshanna episode until the 2009 series.
I also think subtitles were avoided because if this was for the same age group as the regular show, they wouldn't really be able to read them.
You're right about that. It seems that the first 5 episodes were intended for an older audience, and for the most part those ones seem to focus more on the history and important landmarks in Israel than the second series. That's probably why they were filmed in New York after a while. The second series was for younger audiences, and the newest series is for the youngest of all, leaving the dub portion to simple numbers coming from The Count.