I remember reading that on brewingtechniques and IIRC it had something to do with the laminar flow on the bottom of the cooler and channeling. It doesn't make sense to me without going back to look at it, because the wort has to drain through the grainbed to reach the bottom of the cooler, at which point a laminar flow doesn't look like it would hurt anything (as it would if it were down the side, i.e., channeling around the grainbed).
I went with down for mine and it seems to work fine, as well as it seems to be the conventional wisdom these days. BT appears to have 'shutdown' around July '04, and many of the articles are from before that, so it's possible there are new ideas/thoughts on some of the topics.