Now, there's a way through IronTubeHax. Thanks so much to Asia81, Brewzip and Doumekxkai, for the original method and files: http://gbatemp.net/threads/tutorial-savedatafiler-pok%C3%A9mon-shuffle-free-diamonds-and-coins-golds.393568/
1) Download the Save Manager app, and put it inside the 3ds folder on your SD card: https://dl.dropboxusercontent.com/s/6vwld0sg4pkkvcp/save_manager.7z
2) Download and install Python 2.7 on your PC. Google it, should be the first result.
3) Download the Pokémon Shuffle Save Patcher, it's a Python script: http://jheberg.net/captcha/pokemonshufflesavepatcher/
4) Through Save Manager, dump your Pokémon Shuffle save (you choose the desired game to dump saves pressing left and right).
5) Put your 3DS SD card on the PC, open the "SaveDataBackup" folder - a file named "savedata.bin" should be there. Make a backup of it now.
6) Drag and drop the savedata.bin on the downloaded Save Patcher.
7) Remove the old savedata.bin , and replace the updated savedata.bin on the SaveDataBackup folder.
8) Put the SD back on your 3DS, open the Save Manager Homebrew and restore the Pokémon Shuffle save.
You should have now a big amount of Jewels, Mega Speedups, battle items and hearts. Some of them will display huge values, but after using just one of each, they will drop into valid numbers (99999 for coins, 150 for Jewels, 99 for everything else).
For hearts, after they drop into zero, just use one more and the counter will "reset" into 99.