I wouldn't consider Nintendo to be against homebrew / indie games at all. They just want to protect their brand and IPs which is understandable as they're going for mostly a family friendly market and want to preserve quality. Of course they aimed to keep tight control over NES software when it was current gen. For new games on old hardware I honestly don't think they care. It's obviously not their product and legally I don't think they can stop indie NES carts anymore. Unless someone either uses their IP or branding it's not worth their recources and would do more damage to the fanbase than good. If NesMaker was using graphics from licenced Nintendo games for example or encoraging fangames, that's where they would take issue but NM are totally against that.
The only cease and desists I've heard of recently are the Metroid 2 remake AM2R and the Etika Joycons which unfortunately both infringe their intelectual property. You can't really blame Nintendo for that. It doesn't matter how good the product is or the reason behind it, the only person to blame is the one ripping off their stuff.
There's no way NOA don't know about NM but I doubt they'd suddenly start licencing NES games (unless they're limited run re-releases) for several reasons.