Reputational damage. Big part of the appeal of consoles is “it just works”. That falls apart of you start letting random shovelware devs ship whatever.
Having access to the SDK doesn't
give you unfettered access to publish on their stores. It only allows you to write and compile code targeting their hardware/runtime.
No, that's a different concern entirely. Nintendo could (though never will) open up Switch development to everyone while still exercising judicious control over which games are listed in their own store.
And in the meantime, there's already tons of crap shovelware on the Switch storefront. Nintendo doesn't filter for quality.