My first question would be, are you sure it's actually too long? Did you measure it against a mast that you know is right? The reason I ask is that the original Hobie 16 comptips (around 1986) didn't connect to the mast at the tang the way the current ones do. The originals were shorter and there was a section of aluminum mast that extended above the tang. If the mast has been sailed this way for the past 20 years, it would make me wonder whether it is really wrong. Or did the boat originally have one of these shorter comptips which eventually broke and was replaced with a new longer comptip without shortening the aluminum mast?
In any case, the first thing I would do would be to take measurements off a mast you know is good. Make sure the mast is in fact too long.
If the mast is too long, I suspect cutting the tip off the comptip would be the best bet. Then redrill and reinstall the fittings. You may have to deal with moving the plug (I don't know how far down it is on a 16) and resealing the top.
sm