Short answer: Kinda.
Long answer: Your console logs plenty of things and once it gets back to Nintendo you might get banned if you did something you shouldn't be able to if you use the console the official way. There are a few ways to get banned for using MIG Switch - incomplete/mixed/public dumps, playing the same game with the same keys at the same time as another player, etc. I made a post
here about pros and cons about using the MIG Switch. That should give you an idea on whether you should find MIG Switch useful or not.
If you've used your MIG Switch incorrectly (i.e. running incomplete/mixed/public dumps) your activity is already logged and the next time you connect to the Nintendo servers your console will be flagged for ban at best. Staying offline is pretty much delaying the inevitable in that case.