I had the exact same issue. I also had a 3DS LL old from Japan that I changed to the EU region. I wanted to download and use Pokémon Bank but couldn't access the eShop. I managed to install it from a CIA, but it wouldn't connect online. I also tried logging into both my Japanese and European NNIDs and neither worked.
For anyone with the same issue, I have a workaround. You need to create an emuNAND backup of your 3DS using Godmode9. Then, change the region on the emuNAND back to Japan. Boot the emuNAND by holding L and power on and log into a Japanese NNID. If you're logged into a non Japanese NNID you'll have to create a new one based in Japan. Once you do that you can access the eShop again.
To switch back to English, just power the 3DS on while holding L.
For anyone with the same issue, I have a workaround. You need to create an emuNAND backup of your 3DS using Godmode9. Then, change the region on the emuNAND back to Japan. Boot the emuNAND by holding L and power on and log into a Japanese NNID. If you're logged into a non Japanese NNID you'll have to create a new one based in Japan. Once you do that you can access the eShop again.
To switch back to English, just power the 3DS on while holding L.
