Currently there is only one extension hardware named CYBER Save Editor can cheat on 3DS game, but it just still available for Japanese Version Games...
http://gbatemp.net/threads/cyber-gadget-save-editor-for-3ds.347783/
I think the data of play times should be stored on 3DS system RAM ,I have backuped all of the data on SD card,then I played one time,and restore all of the data to SD card.THE 3DS system still shows that I have played one time >_