Soundhax was released a few days ago, allowing homebrew access on the latest 3DS firmware: 11.2. This allows the use of save editors like PKHeX and ROM hacks using HANS.
From Smealum's homebrew website:
It is very likely that this vulnerability will be patched in the next 3DS update, so if this interests you, do not update your 3DS until further notice.
Until now, anyone with an 11.2 3DS would either need to get a hard mod or find an already-hacked 3DS in order to reliably manage save files for use with PKHeX or play ROM hacks. These requirements are no longer applicable thanks to the 33c3 conference revealing several 3DS exploits today. Here are some highlights of its findings as it relates to the 3DS:
If you read either of our save management guides (NDS or 3DS) and needed to purchase additional hardware, you are advised to wait until these exploits are released before actually buying anything. While your purchase would likely still do what you want it to do, free alternatives are coming soon.