I think you'd honestly have to try it or see if YifanLu knows. The version patch definitely, the S/N and region I can't answer.
Though my own question in yifan_lu's direction if they know: Does secureinfo have any other identifying information than the S/N, and if so is it used? Basically, could I patch my N3DS S/N in and safely use a NNID despite it being a public info?
No, it would probably be the opposite. I can check-in on Pokemon Shuffle on my O3DS without being on the newest version (9.6, for example). Many NNID interactions don't require being on the newest update. It seems the ones that involve transfer of funds (eShop purchases/System Transfer/Theme purchases, however you can BROWSE the theme shop without being on the newest version...) tend to require newest software version.
My worry is if I get this to work with the S/N patch settings (using the Japanese serial number), then I would also have to do these steps every time I even check-in with Shuffle. However, if the step to patch the SOAP region returns to USA is needed for every NNID transaction (even for things like Shuffle check-ins), then it doesn't matter...
EDIT: FYI, I'm using a SecureInfo file from a New 3DS XL US that I specifically purchased for this purpose, so using that SN in general should work fine (nothing important tied to it), I just hope to only have to do these patching steps when I actually purchase things...