That's not how DNS works, it's nothing like that at all!
A DNS does DNS lookups, provide you the IP address. A DNS lookup takes a couple of milliseconds, if even that. It only does it when it needs to find something new. Once YOUR DNS (router, or your Switch local routing table for example) knows what to do, it doesn't even use
90DNS anymore. You don't download things via
90DNS, your Switch does it directly to provided IP. It's not a PROXY!
No, this doesn't mean Nintendo have access to your Switch, since
90DNS never provided the way to access them in the first place, so your local DNS have no idea where to go.