You’re spot on with your assessment of Nintendo wanting to sell nostalgia through the Switch store, so it doesn’t make sense to let people access them via the cheaper NES classic; it’s a walled-garden mentality.
But, one could argue they could have kept separate catalogs on the NES classic with juicier titles restricted to the Switch’s store. On that point, do not forget that the NES was quickly hacked to support all other kinds of games to be emulated on it. Nintendo have been one of the fiercest combatants of piracy and hacking in the gaming space, so I am not surprised they pulled the plug on the NES Classic once it was hacked. Who would buy a Switch to buy an eventual copy of, say, a Castlevania game, when it could be loaded up on a hacked NES Classic and played in your living room?