You have a basic misunderstanding of how digital signatures work. When you purchase a game, in one way or another Nintendo combines both your unique identifiers and the common code for the game, uses some mathematics that have been proven for over 4 decades now, and distributes a certificate to you that contains "Deathscreton," "Fortnite," and most likely your console's serial number, and signs it with their eShop private key. When you play the game, your console essentially does the same thing, except it takes its own data about the game and yourself and then signs them with something unique to the console.
The thing is, you cannot simply use CFW or something to get in the middle of transmissions and send the Fortnite certificate when (for example) Zelda code is running, because Nintendo is still going to be checking the game data from your console, and they'll see a Fortnite certificate being sent along with Zelda code. Therefore, a mismatch — Nintendo would see that the running game is NOT what they expect. I don't know exactly how Nintendo does their verification, but it's safe to assume it's not easily flawed.
What Microsoft did with the Xbox 360 (which made piracy very difficult — not impossible, but very difficult) was measuring the actual distance between two different points on a disc, sending those to Microsoft, and then getting banned if they were not what Microsoft expected. The Switch doesn't use discs, but it could do something very similar by simply reading and sending Nintendo random bytes of code from the game on command. If the bytes are indeed randomly chosen there'd be no easy way to fake it out, and the only "hard" way I can imagine would still require you to keep Fortnite essentially "in memory" while playing Zelda, in my example.
The fact is, it's a game of cat & mouse, and unless they did something very wrong they can go as far as changing their verification methods with every update to throw things off. Chances are high that you'll have to buy a second Switch if you want to be able to both pirate games and play online, or at least have some sort of dual-boot setup that completely breaks internet access when booted into "modded" mode.
