The knobs in the down position to bring in the reed bank seems the more logical to me for a couple of reason:

1) the majority of boxes the stops stay in place due to friction, the more times you pull them up and push them down the more the parts wear and the friction decreases. If they are in the down position then they don't need to be closed to be put back in their box and you only need to pull them up to shut off a reed block.

2) For effect it's nicer to go from a thiner sound to a fuller sound and it's a **** sight easier to bring a bank of reeds in by pushing down rather than by pulling up whilst playing.

Personnally, I love the sound of just the 16' and 4' reeds - almost sounds like you're playing two instruments at once

My guess is that the knobs are pull for on and push for off is that Organs with stops work the same way. My mother-in-law has one of those antique reed organs that you pump with your feet, kinda like the way the old sewing machines worked. It has reeds and stops and is really kinda like a great big accordion. And, if you wanted certain reeds turned on, you pull out the stop.

This motif even shows up as the standard metaphor: "Pull out all the stops". It is not "Push in all the stops".

Which isn't to say that it can't be the other way, and there are some accordions that are built the other way. So the choice seems to be arbitrary. I'm just saying that is maybe where the convention may have come from.

-David