FYI, I retail encrypted DevMenu and posted it to that one site that shall not be named and got one report that it worked. The key is that you need CFW and that the rom in question needs to be retail encrypted.
For those who have access to CFW, I would like to you go over and check it out. I can't link to DevMenu. BUT I can link to this:
FBI_Sky3DS.rar
I built that earlier today. Would like to get some feed back on if it boots correctly on Sky3DS while in CFW. I don't personally own a Sky3DS, so can't test these myself.
YOU CAN NOT USE CUSTOM ROMS ON 9.3+ SYSNAND! You need to be in a CFW that patches out sig checks. CakesFW/ReiNand/rxTools for example. So sysnand must be on 9.2 or less.
So I shall repeat that to avoid confusion. If this works, then it's possible to run rom hacks, repacks of eShop games, homebrew, etc on Sky3DS. The only requirement is that the CXI containers inside the 3DS files use retail encryption. Because CFW does not enable zero key encryption (Gateway mode is the only CFW that does and Classic Mode does not allow unsigned content. Though that may have changed with their recent updates to the multirom menu). Hence anything you would want to run on it needs to be retail encrypted to the Secure(0) key. (Newer encryption methods work too, but Secure(0) would have best compatibility)
Also in that rar file is a CIA build. But that's optional. That CIA I built WILL INSTALL TO NAND. USE WITH CAUTION IF INSTALLING TO SYSNAND!
I have successfully built custom system titles (CIAs that will install to NAND) like DevMenu and SaveDataFiler and tried it with homebrew as well. FBI seems to work just fine as a system title.
At the moment it you wouldn't really need to install FBI to nand in this manner unless you plan to do a system format or using future CFW based on Arm9LoaderHax. The 3DS file is the focus here and why I mentioned it.
So retail encrypted roms + CFW means you can run rom hacks, eShop games, and homebrew on your Sky3DS+.
If you want to attempt this your self. Simply get your hands on d0k3's build of Decrypt9 (He calls it Decrypt9WIP). Give it the CXI's (make sure they are unencrypted first) in a folder called D9Game on your SD card, fire up Decrypt9WIP, go to last menu on the bottom. (The "Game" menu) and you'll see it as the second menu option. The NCCH container Encryption option. Use that to encrypt the CXI/CCI files you place in D9Game.
Decrypt9WIP can encrypt 3DS files as well so you don't have to work with CXIs. Encrypting CXIs on their own is only really necessary if you are converting eShop games into CCI games. Note that you'll need to fix the exheader so that it has the SD flag at offset 0x0D disabled. Usually for non SD games like system titles or games running from CCI (3DS roms), it's set to 01. Only ever set it to 00 if the .code inside ExeFS is uncompressed. For just about all retail games, the .code is always compressed.
You can edit the exheader while it's still in the CXI, but note that the offset to be changed will be different (it will be shifted down a bit due to CXI header and other stuff). Anyone familiar with working with hexeditors shouldn't have trouble finding it.
Normally editing the exheader while it's still in the CXI would break hashes. But Decrypt9WIP has to change exheader anyway to change information regarding the keyslot being used for encryption and what not. So it automatically corrects the hashes during the encryption process. So in most instances you don't need to extract exheader or repack the CXI. Try to avoid repacking the CXI. But if you have to, I recommend you repack with with 3DS Builder (specifically the "no crypt" version that AHP_Person made. But you may have trouble finding it. Good luck with that.
). Normal build of 3DS Builder zero key encrypts the CCI containers and as far as I can tell, Decrypt9WIP can't decrypt them. (I get a failed error when I attempt it). Decrypt9WIP will skip things that are already encrypted. Decrypt9WIP doesn't' yet recognize zero key encrypted stuff correctly.
Decrypt9WIP had the encryption feature for awhile now. It's main purpose was to crypto fix games. But in this instance it can be useful for Sky3DS+ users who have CFW.
Theoretically stuff like this will work in the older red/blue button Sky3DS. But no official templates exist for homebrew/eShop games, so good luck with making your own.
Though rom hacks of existing games can use existing templates. Also I can't guarantee every eShop game would behave well on Sky3DS. Mainly due to how saves are handled. If you can try to build the CCI as a card2 save type. I hear Sky3DS gets along with those better.