You might be able to do a DSiware method if you already have a CFW 2DS, you might want to look into it. I would recommend getting a flashcard with NTRBoot, just because it is nifty to keep around.
Firmware would be on the motherboard itself, I don't see why it would be incompatible. The 3DS is newer hardware that is also vulnerable to a motherboard swap.
I ended up getting a V.3. The nice thing is you can pop it out to load files for the Vita, so you don't have to FTP or connect the whole Vita to the PC.
They will probably EOL the 3DS line as soon as the Switch platform is big enough to support Nintendo. They will claim the 3DS line will live just like the ds was a "third pillar".