But the eShop is a system title, not a user-downloaded application, which would be treated quite differently.They are related. As you try to connect with an outdated eShop (i.e. with a bad protocol or whatever), Nintendo thinks that eShop wasn't downloaded properly.
To be clear, I believe you when you say it doesn't work, but I think you're jumping to conclusions with the explanation. What's more likely is that we're either (A) not patching NIM properly, or (B) there's something else in NIM which needs to be patched.
And I say this especially because I know that other people have gotten the eShop to work by patching NIM.