As someone who bought a Steam Deck almost entirely for the purpose of handheld emulation who also owns two Switches, I can tell you that most of the emulation scene on the Deck is very much /not/ Switch games. It's mostly people emulating games from the NES, SNES, N64, Dreamcast, PSX, and similar older systems. Most of these games would do well if they had proper re-releases with updated graphics quality, but the releases we have seen (on PC anyway) have mostly been the original game with an inferior emulator wrapped around it, being resold without any improvements. Square/FF games have been especially guilty of this sin on PC, and pretty much muddied the waters.
Meanwhile, Nintendo has been smarter on Switch, shipping first-party emulators for NES and SNES (but without the games people actually want in the catalog), and has convinced Square to re-release Seiken Densetsu 3 with an official English translation on the Switch w/ the full Mana Trilogy, which I bought and paid for, even though I could emulate all three games because they had improved graphics and an official translation.
I think the concern you have here is wildly overblown, and for the most part there are a tiny tiny tiny amount of people who are pirating Switch games by running them in emulators. Most Switch piracy is happening /on the Switch/ by people running games off the SD Card instead of buying carts/downloading officially, using patched OS / loaders. Nintendo basically killed this for Switches made after the first run in the first generation, and it's even a non-issue.