Naked Jumps are an inherent part of Skydiving Esprit - They are almost an initiation into the intermediate skydiving world. Part of the reason it has become traditional to do it on your 100th Jump is because of Air awareness and ability to deal with extraordinary circumstances being easier. Also its rather liberating, crossing over a line of convention is partially what makes skydiving so special.
As for what happens to the 'equipment' don't worry about it. It'll be there when you land, just make sure those leg straps are nice and tight.
Blue Skies and warm weather!
Brad.