I was just making my own little hack for my Leaf Green, and so I made a new map, easy. I made the warps, works perfectly. So I had put legendary pokemon in my new map, works fine.
I TRIED to hide Master Balls, Rare Candies and Nuggets... Did not work as well.
Any help would be appreciated =)
If you want them invisible: Create a signpost and then select 'Hidden Item'. Now you just have to choose Master Balls, Nuggets and Rare Candies
If you want them to be inside Pokeballs, script of copy an offset from somewhere else