Fortnite is a bit different since it's treated as the character canonically being in the story. Minecraft is a cameo in comparison. However, let's also note that it was the Halo Mash-Up Pack that got on the Nintendo version of Minecraft, something not even the PlayStation version got. So that's actually pretty big in terms of how well Microsoft and Nintendo work together.
Overall, yes, it counts. We also know a Nintendo appearance isn't required, but really damn nice to have. In this case, Master Chief still has it(even without Minecraft alone, Fortnite sealed it the second it's treated as the actual character, not just a skin). So it's not a cameo in FN. It's only a cameo in Minecraft(barely one, though, due to it being a full pack. It's treated as a much bigger thing than a simple cameo, but it's a glorified one at that point).
His chances are still good, but business can still matter. If no plans for Halo to come to a Nintendo console is a thing, this could make him less desirable too, since it's automatic advertising. Banjo-Kazooie is a unique case where it was a Nintendo game at one point, and Sakurai was still able to directly promote Microsoft anyway. Master Chief however is a much more modern character, and they had already cancelled a planned Halo game at one point. Why is this relevant? It means they might not want Halo directly to appear on Nintendo. Does that actually mean a character is impossible? No. It just means it's harder to see Nintendo agreeing from the details we have.