If your game is tiny, I think this would be a delightful collectors edition! If it becomes too many floppies though it becomes a bit too much like clutter IMO.
This is a good point. Even most of the smaller games produced today are usually close to 50 MB. And that could eat up close to 30+ 3.5 floppies. Unless your game can be squeezed or scaled down to fit on four to five floppie disks, it's not going to fly.
A somewhat better idea would be to include a "collector's edition" instruction booklet with the boxed copy. I've always really appreciated properly done instruction booklets. I am reminded of the "Guidebook to the Land of the Green Isles" from King's Quest VI. Easily one of the best and most creative instuction booklets I've ever seen, and well worth the trouble of obtaining a physical copy of the game.