It wasn't planned. There was no airbag or something to cushion the fall. Those foot-holes always been there on every cage match in case the performers want to go up top. Vince legitimately freaked out when Shane went and done that madness. Undertaker just played along as a performer but his reaction from the aftermath said everything when the camera zoomed up to his face at Wrestlemania. The execs expected Shane to cut part of the cage and that was it, but jumping off the very top to land on a desk?! Shane IS a madman. He always has been because he is unpredictable and make up his own rules as he goes along. I think the only person that understands his madness is Kurt Angle..
Not only that, but we have seen many times where you can miss your mark.
You can miss the table, you can miss the clean hit