I've been creating tons of cool pixel art and making recreations of retro games I'm getting from badge arcade. But I've recently run into this issue and I'm wondering if there's some sort of homebrew out there that bypasses this restriction.
The 300-icon limit? Google around and you will find heaps of griping about it. The closest thing there is to a solution is 3dsbank, which basically lets you swap out different "Nintendo 3DS" folders but still won't let you have more than 300 items at the same time.
Don't forget that items in folders count against the limit too.