Any legitimately purchased CIA's should transfer, however, legit CIA's (the ones that can be installed on any system) don't transfer in my experience, as well as any that aren't properly signed. I've heard that preinstalled games only transfer if you linked a NNID to the console.
It depends. Do you ever want to use Ninjhax again? Or any modding? Because system transfer required both consoles to be updated to the latest version, so you will lose access to all current exploits.
I think that should work, however, I think the eshop accounts are tied to the NNID, or console if you don't have NNID, and when you system transfer it transfers the software license/NNID to the new console. So the eshop accounts are separate and you won't be able to redownload on the original console. They stay on the original console if you restore emuNAND, but I think on the original console if you go online it may try to check the licenses and see that it has been transfered, so it will delete them on your original console. And since you can only have one console tied to an NNID, it may cause problems if you have 2 devices with one NNID. So it may only work if you keep your original 3DS completely offline.
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