On one hand, this isn't a particularly new thing, as highlighted by your example of Zelda content in other games. Especially when using Smash Bros, inherently a Nintendo-based crossover franchise, and remakes to illustrate your point. Before the GameCube hosted a ground-up Zelda game, we already had Zelda content in Melee and Ocarina of Time Master Quest, plus Soul Calibur II released right on top of Wind Waker.
On the other hand, I can see a distinct difference here. Link appearing in Mario Kart is a lot different from Smash Bros or a Zelda remake. It's even different from Soul Calibur II in that it's a first-party title. Then you have Bayonetta, Tekken Tag Tournament, Monster Hunter 4, etc, where the 'guest appearance' isn't by Link himself (as was the case in Soul Calibur), but simply a costume worn by another character to emulate Link. I think I prefer the former case, where it feels like Nintendo is expanding their own universe -- especially since making him DLC makes Link feel more like a guest character than a permenant fixture in the series.
I think the Samus love in Bayonetta and Monster Hunter is a better example. It's proof-positive that the franchise is still on Nintendo's mind, still on the burner, even though there hasn't been a release in the series (new or remake) in over 4 years. Contrast it with the abundance of Captain Falcon or Ness costumes in these collaborations... hmmmm........ yeah.