The switch no, your account maybe.
Simply put if you plan on using these pokemon to play online battles coop etc if they are not legal pokemon (meaning all the Metadata is correct) you could be banned, if you use an editor like pkhex to mod pokemon they will usually warn you if and when the pokemon isn't legal and even tell you which parameters are impossible but it's not perfect. If you're playing the modded nx without cheats etc then everything you catch should be considered legal and not get you flagged when traded and used. If you used a cheat to say catch a Mew or a pokemon that is from the opposite version of your game or not in them at all it would still be very illegal but then again are you gonna use it online ?