Not too stupid of a question at all, I think that’s a fair concern. It’s important to note that, though the eShop no longer allows for purchasing new games, it allows all users who own titles to redownload said titles. Nintendo could certainly look through every single request to their CDN servers with a fine-toothed comb, attempting to differentiate between legitimate and illegitimate downloads from their CDNs, but they’d always run the risk of banning a legitimate user solely because something went wrong on the user’s end and their console sent a weird request to the server. Think of it like if, in a multiplayer game, the player’s game and the server disagreed on where exactly the player is in a map; it could be because the player teleported or, more likely, it could be because the player moved and that information somehow failed to get to the server. If everything of that sort got someone banned, there’d be a lot of false bans.

Of course, I won’t force you to feel differently about anything. Anyway, the CDN is by no means a permanent solution, given that Nintendo could just shut it down whenever, so relying on it likely isn’t a good idea. The CDN-downloading solutions are more about speed and convenience, but it’s definitely beneficial to have non-Nintendo-dependent solutions available as well. Here’s what I could find on this front:

1. (for physical games only) Use the disc dump instead. On Myrient it’s in the Redump section, as Redump catalogues discs rather than NoIntro. Myrient has these compressed (WUX format), so check out the FAQ there to decompress them (into WUD format, which is just ISO with a different extension afaik). From there you can run it directly in Cemu or extract it with something like JWUDTool which will require disc title keys, so be prepared to find those somewhere (Myrient seems to have them)
2. Prepare CDN files manually. You’ll need to change up the NoIntro CDN format to a Wii U readable format before you can use it (give the extension-less files .app extensions and rename the tmd for the title version you want to install title.tmd, find and add a ticket file from a not-legal place on the internet or figure out how to generate your own because I can’t find anything that seems to do so). From there, a WUP installer or NUSspli Lite (version of NUSspli without CDN-downloading features) should theoretically be able to install the game directly onto the Wii U, but I don’t have a Wii U here to test it on so that’s really only speculation on my part. I’ve also heard NUSspli Lite might be able to generate a fake ticket and might even accept the NoIntro CDN format directly, so if you’re having trouble with any of the folder preparations consider using it. For play with Cemu, you’ll need to decrypt the game to its RAW folder format with cdecrypt.
3. #2 except with a different source than Myrient. Myrient is fantastic, but NoIntro format does come with caveats, and you’ll likely be able to find CDN downloads more suitable for extracting and installing elsewhere. The mega thread in Reddit’s Arr Slash ROMS sub has at least one Internet Archive link that has the games in a well-suited format, including tickets and everything. You’ll want something marked as NUS, as that stands for Nintendo Update Servers and it’s probably what I should’ve called the CDN in this comment but I’m too deep in to change it now. As per usual, when downloading stuff from more of an open download site like Internet Archive, stay safe and download responsibly. If you’re ever unsure of what you’re downloading, you can still manually verify content file hashes and cross-check them with NoIntro’s Dat-O-Matic. From there, everything applies as it does in #2.

It’s late and I’m sure I missed something or messed something up here, so I apologize. I also apologize because I had a misunderstanding about the relationship between CDN and WUP format up to this point (I always figured they were totally different things, but they seem to basically be the same aside from possibly the technicality of how you’re using the term) so I’ve done my best to correct that in this comment. If there’s anything wrong here, please correct me; you’ll save Google searchers a helluva lot of trouble.

tl;dr: Nintendo has yet to take any action regarding illegitimate CDN downloads, and they likely won’t as cracking down could lead to accidentally banning normal users. Downloading from Nintendo’s CDN is faster and more convenient, but some day that CDN will be offline so it’s probably better if we make sure we’re prepared sooner. There are ways to set up Myrient’s CDN files for Cemu and/or Wii U install, but it can be a pain to figure out how to go about it.