It's 2 completely different things.
Updates won't get deleted. DLC gets deleted.
You are partially right that DLC don't get wiped. That applies to some games only for some reason and some not. But it has nothing to do with linking and unlinking nands. That's only for the data management bug.
Some examples:
- try installing Super Smash DLC, then go to eshop. It WILL get erased.
- Themes are a type of DLC. It will also gets erased everytime you got to shop.
- street plaza dlc, Final Fantasy Theatrythm and curtain call, they all don't get deleted when getting into eshop.
As for what others were suggesting, modifying any .dbs file won't change anything. The correct info is what @EmanueleBGN mentioned above: eshop checks the data you own when you connect. But I think he's wrong on the legit CIA part. I don't think those get deleted
M'kay, loaded up SSB - Mewtwo - Ryu - Luca / Hyrule Castle - yada yada. > Closed out > Logged into eshop > Closed > SSB > Everythings still there. :|

